Wordpress Update / Plugins Page Very Slow
As of late, a development site (towerofgreed.com/ - I now use vagrant, don't worry haha)I have has become extremely slow on the admin-side, specifically the plugins / update core page. It took about 30-60 seconds just to load http://example.com/wordpress/wp-admin/update-core.php, which is quite odd. The plugins page itself is hit or miss, sometimes it's quick, sometimes it takes forever.
The site itself loads in about 0.6-1.2 seconds, where as specific admin pages take over 30 seconds (chrome extension reporting these times), so it's definitely something related to the admin / plugin screen, but I have no idea what.
I was hunting down a bug with a plugin awhile back, but that's disabled on the site now, and this particular issue is still persisting. The formally mentioned bug was an odd one where a very specific plugin seemed to be causing the entire update (plugins or core) to completely time out, where as removing it got rid of said issue; the weird part, is that it's for "shortcodes ultimate" (a popular plugin), and it's just the skins add-on (core plugin doesn't seem to have this issue).
Obviously related to the issue, is that updating plugins can often times hang, they'll complete, but take 30+ seconds to work, where as other times / plugins will update in a flash. Upon testing now, even reloading the main Dashboard page can be super slow, though it's random, and often loads in a split second (0.5 - 1 seconds). Coincidental or not, slow loads always seem to come out to 38~ seconds.
I don't know if I'm chasing a ghost, or if something is more fundamentally wrong, so any direction would be nice - any ideas?
Specs / info to the best of my ability: (I set this up so long ago, and am just now learning it - I'm due for a refresher and might just start from scratch again)
MariaDB (replaced MySQL when learning about optimization)
No Caching of any kind (disabled while in development)
I believe I use PHP-FPM, whichever is commonly installed via the beginner guides floating around here for a LEMP stack
Root user is disabled for security reasons (followed a tutorial on here)
www-data is what executes PHP, so most files are owned by www-data:www-data, where as theme files are wp-user:wp-user, which belongs to Wordpress, and allows me to update via FTP (this all confuses me, but has worked for quite some time, and I've corrected mistakes in the past). I for the most part get the difference between my wp-user, and www-data, but I don't always know when to use one or the other, what Wordpress requires on which files, etc, which occasionally causes issues updating plugins, odd files (not in the plugin folder, due to the way the plugin handles files), etc.
The rest is just up to date Wordpress, minimal plugins (I try to keep a very vanilla install, as I hate bloat), and the Genesis Framework, which is quite vanilla itself.