Multisite Dashboard: 500 and other errors

So I’ve made some progress since my last thread. I run my site (orenstransitpage.com) from a wordpress directory in the root of my site. However, in order to access anything on the Network dashboard, I have to add in /wordpress/ to the URL. For example, https://orenstransitpage.com/wp-admin/network/users.php results in a 500 internal server error, but if I change it to https://orenstransitpage.com/wordpress/wp-admin/network/users.php it loads fine.

Here is my .htaccess file:

# Use PHPBETA as default
AddHandler application/x-httpd-phpbeta .php
## EXPIRES CACHING ##
<IfModule mod_expires.c>
ExpiresActive On
ExpiresByType image/jpg "access 1 year"
ExpiresByType image/jpeg "access 1 year"
ExpiresByType image/gif "access 1 year"
ExpiresByType image/png "access 1 year"
ExpiresByType text/css "access 1 month"
ExpiresByType text/html "access 1 month"
ExpiresByType application/pdf "access 1 month"
ExpiresByType text/x-javascript "access 1 month"
ExpiresByType application/x-shockwave-flash "access 1 month"
ExpiresByType image/x-icon "access 1 year"
ExpiresDefault "access 1 month"
</IfModule>
## EXPIRES CACHING ##

RewriteEngine on
RewriteCond %{HTTP_HOST} ^orenstransitpage\.com$ [OR]
RewriteCond %{HTTP_HOST} ^www\.orenstransitpage\.com$
RewriteRule ^orenstransitpage\/?$ "http\:\/\/orenstransitpage\.com\/" [R=301,L]

RewriteRule ^(orenstransitpage/.*)$ https://orenstransitpage.com [R=301,L]
RewriteRule ^(otpamtrakpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/amtrak/ [R=301,L]
RewriteRule ^(otpbospics/.*)$ https://orenstransitpage.com/transit-photography/united-states/boston/ [R=301,L]
RewriteRule ^(otpbrusselspics/.*)$ https://orenstransitpage.com/transit-photography/europe/belgium/ [R=301,L]
RewriteRule ^(otpbudapestpics/.*)$ https://orenstransitpage.com/transit-photography/europe/hungary/ [R=301,L]
RewriteRule ^(otpbveroutes/.*)$ https://orenstransitpage.com/ [R=301,L]
RewriteRule ^(otpchipics/.*)$ https://orenstransitpage.com/transit-photography/united-states/chicago/ [R=301,L]
RewriteRule ^(otpdccars/.*)$ https://orenstransitpage.com/transit-photography/united-states/washington-dc/ [R=301,L]
RewriteRule ^(otpdisneypics/.*)$ https://orenstransitpage.com/transit-photography/united-states/disney-worldorlando/ [R=301,L]
RewriteRule ^(otpeastcoast/.*)$ https://orenstransitpage.com/transit-photography/united-states [R=301,L]
RewriteRule ^(otpegyptpics/.*)$ https://orenstransitpage.com/transit-photography/middle-east/egypt/ [R=301,L]
RewriteRule ^(otpgermpics/.*)$ https://orenstransitpage.com/transit-photography/europe/germany/ [R=301,L]
RewriteRule ^(otpistanbulpics/.*)$ https://orenstransitpage.com/transit-photography/europe/turkey/ [R=301,L]
RewriteRule ^(otpitalypics/.*)$ https://orenstransitpage.com/transit-photography/europe/italy/ [R=301,L]
RewriteRule ^(otplondonpics/.*)$ https://orenstransitpage.com/transit-photography/europe/united-kingdom/ [R=301,L]
RewriteRule ^(otplvivpics/.*)$ https://orenstransitpage.com/transit-photography/europe/ukraine/ [R=301,L]
RewriteRule ^(otpmartapics/.*)$ https://orenstransitpage.com/transit-photography/united-states/atlanta/ [R=301,L]
RewriteRule ^(otpnetherlandspics/.*)$ https://orenstransitpage.com/transit-photography/europe/netherlands/ [R=301,L]
RewriteRule ^(otpnjpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/new-jersey/ [R=301,L]
RewriteRule ^(otpnortapics/.*)$ https://orenstransitpage.com/transit-photography/united-states/new-orleans/ [R=301,L]
RewriteRule ^(otpphilpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/philadelphia/ [R=301,L]
RewriteRule ^(otpparispics/.*)$ https://orenstransitpage.com/transit-photography/europe/france/ [R=301,L]
RewriteRule ^(otppolandpics/.*)$ https://orenstransitpage.com/transit-photography/europe/poland/ [R=301,L]
RewriteRule ^(otpportlandpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/portland/ [R=301,L]
RewriteRule ^(otprideonpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/washington-dc/ride-on/ [R=301,L]
RewriteRule ^(otpseattlepics/.*)$ https://orenstransitpage.com/transit-photography/united-states/seattle/ [R=301,L]
RewriteRule ^(otpsfpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/san-francisco/ [R=301,L]
RewriteRule ^(otpskylines/.*)$ https://orenstransitpage.com/ [R=301,L]
RewriteRule ^(otpspainpics/.*)$ https://orenstransitpage.com/transit-photography/europe/spain/ [R=301,L]
RewriteRule ^(otpstcumpics/.*)$ https://orenstransitpage.com/transit-photography/canada/montreal/ [R=301,L]
RewriteRule ^(otpswitzerlandpics/.*)$ https://orenstransitpage.com/transit-photography/europe/switzerland/ [R=301,L]
RewriteRule ^(otptcatpics/.*)$ https://orenstransitpage.com/transit-photography/united-states/ithaca/ [R=301,L]
RewriteRule ^(otptorontopics/.*)$ https://orenstransitpage.com/transit-photography/canada/toronto/ [R=301,L]
RewriteRule ^(otpvancouverpics/.*)$ https://orenstransitpage.com/transit-photography/canada/vancouver/ [R=301,L]
RewriteRule ^(otpwestcoast/.*)$ https://orenstransitpage.com/transit-photography/united-states [R=301,L]
RewriteRule ^(otpisraelpics/.*)$ https://orenstransitpage.com/which-part-of-orens-transit-page-are-you-trying-to-reach/ [R=301,L]
RewriteRule ^(water-water-everywhere/.*)$ https://orenstransitpage.com/the-travelogue/water-water-everywhere/ [R=301,L]
RewriteRule ^(types-of-transit-photos/.*)$ https://orenstransitpage.com/the-travelogue/types-of-transit-photos/ [R=301,L]
RewriteRule ^(orens-reading-list-the-world-metro-map/.*)$ https://orenstransitpage.com/the-travelogue/orens-reading-list-the-world-metro-map/ [R=301,L]
RewriteRule ^(why-take-photos-of-transit/.*)$ https://orenstransitpage.com/the-travelogue/why-take-photos-of-transit/ [R=301,L]
RewriteRule ^(bus-photo-of-the-month-february-2016/.*)$ https://orenstransitpage.com/the-travelogue/bus-photo-of-the-month-february-2016/ [R=301,L]
RewriteRule ^(rail-photo-of-the-month-february-2016/.*)$ https://orenstransitpage.com/the-travelogue/rail-photo-of-the-month-february-2016/ [R=301,L]
RewriteRule ^(10-new-dc-area-photos-added/.*)$ https://orenstransitpage.com/the-travelogue/10-new-dc-area-photos-added/ [R=301,L]
RewriteRule ^(new-arrivals/.*)$ https://orenstransitpage.com/the-travelogue/new-arrivals/ [R=301,L]
RewriteRule ^(what-is-the-travelogue/.*)$ https://orenstransitpage.com/the-travelogue/what-is-the-travelogue/ [R=301,L]
RewriteRule ^(welcome-aboard-again/.*)$ https://orenstransitpage.com/the-travelogue/welcome-aboard-again/ [R=301,L]

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) wordpress/$1 [L]
RewriteRule ^(.*\.php)$ wordpress/$1 [L]
RewriteRule . index.php [L]
</IfModule>

# END WordPress

# BEGIN Sandbox
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /wordpress/
RewriteCond %{REQUEST_URI} !^/wordpress/sandbox/.* [NC]
RewriteCond %{HTTP_COOKIE} sandbox=([^;]+) [NC]
RewriteRule ^(.*)$ /wordpress/sandbox/%1/$1 [NC,L,QSA,S=10]
</IfModule>
# END Sandbox

I had things working very briefly tonight, but then in fiddling around with a setting things went south and in the process of resetting plugin installations, this new issue came up and I have yet to figure out how to get things back to normal.