permalinks on, no pages work

Turn on permalinks from general > permalinks and select the output there. Do you get the same problem?

Yes, same problem.
That is where it was turned on from before.

Find .htacess in your root folder and make sure this is what it looks like.

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

I guess this is where it gets complicated because I have an existing site and I installed wordpress in a subfolder while I set it up before migrating it.
I need to leave my existing site running and the current htaccess is:

<Files .htaccess>
deny from all
</Files>
RewriteEngine On
RewriteCond %{HTTP_HOST} !^(www\.mysite\.co\.uk)?$
RewriteCond $1 !^cart/updateorders\.php$
RewriteCond $1 !^myscriptpage\.php$
RewriteCond %{REQUEST_URI} !^/(NewSite)
RewriteRule ^(.*)$ https://www.mysite.co.uk/$1 [R=301,L]
php_value memory_limit 256M

any ideas how I can rewrite that t get it to work with the current site?

It is not possible to know since we dont know how your site is setup.

Did you try putting the code in as I put in the folder where your installation is? What happened?

This is the current htaccess

# BEGIN Better WP Security
Options -Indexes

# Begin HackRepair.com Blacklist
RewriteEngine on
#Block comment spammers, bad bots and some proxies
RewriteCond %{REMOTE_HOST} 12.226.240.248 [OR]
RewriteCond %{REMOTE_HOST} 24.111.102.26 [OR]
RewriteCond %{REMOTE_HOST} 24.117.121.113 [OR]
RewriteCond %{REMOTE_HOST} 65.30.216.140 [OR]
RewriteCond %{REMOTE_HOST} 67.87.64.23 [OR]
RewriteCond %{REMOTE_HOST} 68.12.149.198 [OR]
RewriteCond %{REMOTE_HOST} 69.139.167.203 [OR]
RewriteCond %{REMOTE_HOST} 74.95.182.57 [OR]
RewriteCond %{REMOTE_HOST} 91.121.3.29 [OR]
RewriteCond %{REMOTE_HOST} 203.94.229.227 [OR]
RewriteCond %{REMOTE_HOST} 208.96.122.142 [OR]
RewriteCond %{REMOTE_HOST} 210.0.141.247 [OR]
RewriteCond %{REMOTE_HOST} 210.197.97.67 [OR]
RewriteCond %{REMOTE_HOST} 212.179.127.188 [OR]
RewriteCond %{REMOTE_HOST} 216.246.60.183 [OR]
RewriteCond %{REMOTE_HOST} 220.156.189.233 [OR]
RewriteCond %{REMOTE_HOST} 222.36.12.42 [OR]
# Abuse Agent Blocking
RewriteCond %{HTTP_USER_AGENT} ^BlackWidow [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Bolt\ 0 [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Bot\ mailto:craftbot\@yahoo\.com [NC,OR]
RewriteCond %{HTTP_USER_AGENT} CazoodleBot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^ChinaClaw [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Custo [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Default\ Browser\ 0 [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^DIIbot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^DISCo [NC,OR]
RewriteCond %{HTTP_USER_AGENT} discobot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Download\ Demon [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^eCatch [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ecxi [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^EirGrabber [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^EmailCollector [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^EmailSiphon [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^EmailWolf [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Express\ WebPictures [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^ExtractorPro [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^EyeNetIE [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^FlashGet [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^GetRight [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^GetWeb! [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Go!Zilla [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Go-Ahead-Got-It [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^GrabNet [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Grafula [NC,OR]
RewriteCond %{HTTP_USER_AGENT} GT::WWW [NC,OR]
RewriteCond %{HTTP_USER_AGENT} heritrix [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^HMView [NC,OR]
RewriteCond %{HTTP_USER_AGENT} HTTP::Lite [NC,OR]
RewriteCond %{HTTP_USER_AGENT} HTTrack [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ia_archiver [NC,OR]
RewriteCond %{HTTP_USER_AGENT} IDBot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} id-search [NC,OR]
RewriteCond %{HTTP_USER_AGENT} id-search\.org [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Image\ Stripper [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Image\ Sucker [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Indy\ Library [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^InterGET [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Internet\ Ninja [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^InternetSeer\.com [NC,OR]
RewriteCond %{HTTP_USER_AGENT} IRLbot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ISC\ Systems\ iRc\ Search\ 2\.1 [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Java [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^JetCar [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^JOC\ Web\ Spider [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^larbin [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^LeechFTP [NC,OR]
RewriteCond %{HTTP_USER_AGENT} libwww [NC,OR]
RewriteCond %{HTTP_USER_AGENT} libwww-perl [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Link [NC,OR]
RewriteCond %{HTTP_USER_AGENT} LinksManager.com_bot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} linkwalker [NC,OR]
RewriteCond %{HTTP_USER_AGENT} lwp-trivial [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Mass\ Downloader [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Maxthon$ [NC,OR]
RewriteCond %{HTTP_USER_AGENT} MFC_Tear_Sample [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^microsoft\.url [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Microsoft\ URL\ Control [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^MIDown\ tool [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Mister\ PiX [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Missigua\ Locator [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Mozilla\.*Indy [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Mozilla\.*NEWT [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^MSFrontPage [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Navroad [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^NearSite [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^NetAnts [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^NetSpider [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Net\ Vampire [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^NetZIP [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Nutch [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Octopus [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Offline\ Explorer [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Offline\ Navigator [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^PageGrabber [NC,OR]
RewriteCond %{HTTP_USER_AGENT} panscient.com [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Papa\ Foto [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^pavuk [NC,OR]
RewriteCond %{HTTP_USER_AGENT} PECL::HTTP [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^PeoplePal [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^pcBrowser [NC,OR]
RewriteCond %{HTTP_USER_AGENT} PHPCrawl [NC,OR]
RewriteCond %{HTTP_USER_AGENT} PleaseCrawl [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^psbot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^RealDownload [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^ReGet [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Rippers\ 0 [NC,OR]
RewriteCond %{HTTP_USER_AGENT} SBIder [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^SeaMonkey$ [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^sitecheck\.internetseer\.com [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^SiteSnagger [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^SmartDownload [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Snoopy [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Steeler [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^SuperBot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^SuperHTTP [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Surfbot [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^tAkeOut [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Teleport\ Pro [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Toata\ dragostea\ mea\ pentru\ diavola [NC,OR]
RewriteCond %{HTTP_USER_AGENT} URI::Fetch [NC,OR]
RewriteCond %{HTTP_USER_AGENT} urllib [NC,OR]
RewriteCond %{HTTP_USER_AGENT} User-Agent [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^VoidEYE [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Web\ Image\ Collector [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Web\ Sucker [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Web\ Sucker [NC,OR]
RewriteCond %{HTTP_USER_AGENT} webalta [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebAuto [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^[Ww]eb[Bb]andit [NC,OR]
RewriteCond %{HTTP_USER_AGENT} WebCollage [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebCopier [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebFetch [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebGo\ IS [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebLeacher [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebReaper [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebSauger [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Website\ eXtractor [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Website\ Quester [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebStripper [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebWhacker [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WebZIP [NC,OR]
RewriteCond %{HTTP_USER_AGENT} Wells\ Search\ II [NC,OR]
RewriteCond %{HTTP_USER_AGENT} WEP\ Search [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Wget [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Widow [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WWW-Mechanize [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^WWWOFFLE [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Xaldon\ WebSpider [NC,OR]
RewriteCond %{HTTP_USER_AGENT} zermelo [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Zeus [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ^Zeus\.*Webster [NC,OR]
RewriteCond %{HTTP_USER_AGENT} ZyBorg [NC]
RewriteRule ^.* - [F,L]
# Abuse bot blocking rule end
order allow,deny
allow from all
# Start Custom Blocks
# Bluecoat
deny from 8.21.4.254
deny from 65.46.48.192/30
deny from 65.160.238.176/28
deny from 85.92.222.0/24
deny from 206.51.36.0/22
deny from 216.52.23.0/24
# cyveillance (already blocked 38.*)
deny from 38.100.19.8/29
deny from 38.100.21.0/24
deny from 38.100.41.64/26
deny from 38.105.71.0/25
deny from 38.105.83.0/27
deny from 38.112.21.140/30
deny from 38.118.42.32/29
deny from 65.213.208.128/27
deny from 65.222.176.96/27
deny from 65.222.185.72/29
# Cyberpatrol
deny from 38.103.17.160/27
# Internet Identity - Anti-Phishing
deny from 66.113.96.0/20
deny from 70.35.113.192/27
# Ironport
deny from 204.15.80.0/22
# Lightspeed Systems Security
deny from 66.17.15.128/26
deny from 69.84.207.32/27
deny from 69.84.207.128/25
# Layered Technologies
deny from 72.36.128.0/17
deny from 72.232.0.0/16
deny from 72.233.0.0/17
deny from 216.32.0.0/14
# M86
deny from 67.192.231.224/29
deny from 208.90.236.0/22
# McAfee-Secure-Computing
deny from 69.48.241.64/26
deny from 80.66.0.0/19
deny from 192.55.214.0/24
deny from 207.67.117.0/24
# Phish-Inspector.com
deny from 209.147.127.208/28
# Prescient Software, Inc. Phishmongers
deny from 198.186.190.0/23
deny from 198.186.192.0/23
deny from 198.186.194.0/24
# urlfilterdb
deny from 207.210.99.32/29
# websense-in.car1.sandiego1.level3.net
deny from 4.53.120.22
# Websense
deny from 66.194.6.0/24
deny from 67.117.201.128/28
deny from 69.67.32.0/20
deny from 131.191.87.0/24
deny from 204.15.64.0/21
deny from 208.80.192.0/21
deny from 212.62.26.64/27
deny from 213.168.226.0/24
deny from 213.168.241.0/30
deny from 213.168.242.0/30
deny from 213.236.150.16/28
# Yandex
deny from 77.88.0.0/18
deny from 77.88.22.0/23
deny from 77.88.24.0/21
deny from 77.88.24.0/22
deny from 77.88.28.0/22
deny from 77.88.36.0/23
deny from 77.88.42.0/23
deny from 77.88.44.0/24
deny from 77.88.50.0/23
deny from 87.250.224.0/19
deny from 87.250.230.0/23
deny from 87.250.252.0/22
deny from 93.158.128.0/18
deny from 93.158.137.0/24
deny from 93.158.144.0/21
deny from 93.158.144.0/23
deny from 93.158.146.0/23
deny from 93.158.148.0/22
deny from 95.108.128.0/17
deny from 95.108.128.0/24
deny from 95.108.152.0/22
deny from 95.108.216.0/23
deny from 95.108.240.0/21
deny from 95.108.248.0/23
deny from 178.154.128.0/17
deny from 178.154.160.0/22
deny from 178.154.164.0/23
deny from 199.36.240.0/22
deny from 213.180.192.0/19
deny from 213.180.204.0/24
deny from 213.180.206.0/23
deny from 213.180.209.0/24
deny from 213.180.218.0/23
deny from 213.180.220.0/23
# End HackRepair.com Blacklist
<files .htaccess>
Order allow,deny
Deny from all
</files>

<files readme.html>
Order allow,deny
Deny from all
</files>

<files readme.txt>
Order allow,deny
Deny from all
</files>

<files install.php>
Order allow,deny
Deny from all
</files>

<files wp-config.php>
Order allow,deny
Deny from all
</files>

<IfModule mod_rewrite.c>
RewriteEngine On

RewriteRule ^wp-admin/includes/ - [F,L]
RewriteRule !^wp-includes/ - [S=3]
RewriteCond %{SCRIPT_FILENAME} !^(.*)wp-includes/ms-files.php
RewriteRule ^wp-includes/[^/]+\.php$ - [F,L]
RewriteRule ^wp-includes/js/tinymce/langs/.+\.php - [F,L]
RewriteRule ^wp-includes/theme-compat/ - [F,L]

RewriteCond %{REQUEST_METHOD} ^(TRACE|DELETE|TRACK) [NC]
RewriteRule ^(.*)$ - [F,L]

RewriteCond %{QUERY_STRING} \.\.\/ [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(bash|git|hg|log|svn|swp|cvs) [NC,OR]
RewriteCond %{QUERY_STRING} etc/passwd [NC,OR]
RewriteCond %{QUERY_STRING} boot\.ini [NC,OR]
RewriteCond %{QUERY_STRING} ftp\:  [NC,OR]
RewriteCond %{QUERY_STRING} http\:  [NC,OR]
RewriteCond %{QUERY_STRING} https\:  [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} mosConfig_[a-zA-Z_]{1,21}(=|%3D) [NC,OR]
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(\[|\]|\(|\)|<|>|ê|"|;|\?|\*|=$).* [NC,OR]
RewriteCond %{QUERY_STRING} ^.*("|'|<|>|\|{||).* [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(%24&x).* [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(%0|%A|%B|%C|%D|%E|%F|127\.0).* [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(globals|encode|localhost|loopback).* [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(request|select|concat|insert|union|declare).* [NC]
RewriteCond %{QUERY_STRING} !^loggedout=true
RewriteCond %{QUERY_STRING} !^action=rp
RewriteCond %{HTTP_COOKIE} !^.*wordpress_logged_in_.*$
RewriteCond %{HTTP_REFERER} !^https://maps\.googleapis\.com(.*)$
RewriteRule ^(.*)$ - [F,L]

</IfModule>
# END Better WP Security