My dynamic php website doesn't work properly with wordpress

Okay, hope i don’t screw up the formatting. ?? I have a few issues, please bear with me. Link To My Site

1) WordPress displays fine at first, then clicking internal links (IE making a comment) it’s no longer dynamic with my php setup.
2).htaccess is not writable regardless of setting it to the extreme 777 permissions.
3)I believe #1 issue is related to the fact that my site URL is set to https://example.com/Blog. It’s treating ‘Blog’ as a directory when in fact Blog is just a rewrite for index.php?page=blog.php. Also I believe this same issue is causing links in the menu to change. The moment you click on Blog, the links in the menu change from (Home|Blog|Forum..etc) to (BlogHome|BlogBlog|BlogForum..etc)

Site directory

public_html <--real root
    agentc0re  <---pseudo root & main website root
        blog   <---Wordpress installation

My PHP code in my index.php is as follows (sorry for all the comments i reverted it to it’s most simple stage for troubleshooting purposes)

<?php
    //if(isset($_GET['page'])) {
        $page = $_GET['page'];	/* gets the variable $page */
        //$page = basename($page);
    //}
    //else{$page = 'index.php';}
    if (!empty($page)) {
        $page .= '.php';
        /*if(!file_exists($page)) {
            $page = "home";
        }*/
        /*else {
            include '404.shtml'
        }*/

        include($page);
    } 	/* if $page has a value, include it */
    else {
        include('home.php');
    } 	/* otherwise, include the default page */

    //include 'home.php';
    include('menu.php');
?>

What this says. Make index.php into calling pages via index.php?page=
whatever page=, strip the .php off the end for a nicer display. Next include the page IE index.php?page=blog. Other wise include home.php and then finally include my menu.php.

As of right now wordpress “Works” but only because of these rewrite rules

<IfModule mod_rewrite.c>
RewriteEngine On
#RewriteBase /blog/
##RewriteRule ^index\.php$ - [L]
RewriteCond %{HTTP_HOST} ^(www.)?agentc0re.com$
RewriteRule ^Blog/?$ /index.php?page=blog [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /blog/index.php [L]
</IfModule>

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /agentc0re
#
RewriteRule ^Home/?$ /index.php?page= [L]
#RewriteRule ^Blog/?$ /index.php?page=blog [L]
RewriteRule ^Forum/?$ /index.php?page=forum [L]
RewriteRule ^Sub_Counter/?$ /agentc0re/index.php?page=/SubCounter/subCounter [L]
RewriteRule ^AboutMe/?$ /index.php?page=aboutme [L]
RewriteRule ^Contact/?$ /index.php?page=contact [L]
</IfModule>

Explaining #2 issue more is i don’t believe that it’s even reading the .htaccess located in the wordpress directory because of the fact that my siturl being https://example.com/Blog, <–it treas Blog as a directory. Blog does not exists, therefore .htaccess cannot be written. But, Blog is just a rewrite rule that actually calls

index.php?page=blog.php

Where blog.php is just a copy of the index.php inside the wordpress folder except that the require directive is set to,

require( dirname( __FILE__ ) . '/blog/wp-blog-header.php' );

What I want to happen – TL;DR
Have the whole wordpress site load just like how it first loads when you click on the Blog link on the menu for the first time. I want to be able to display my menu/header & have the loading screen present along side wordpress.

Figure out why wordpress treats my site url of ‘Blog’ as a dir instead of a file. I could make a symlink but im not sure if thats the proper way to handle this.

Figure out why wordpress is appending Blog to my menu links.

WOW, i know this is a lot to digest, and I appreciate it if you made it this far. I know there are a lot of problems to tackle but i’ve been posting EVERWHERE & I am hoping someone here can help me out.

Thank you SOOOO very much.
-Jon