404 Broken Links hummingbird, cloudflare,htaccess

I have come across 404 broken links issue shortly after compressing advanced files in hummingbird though it also could have been from something else. All I know is my pages show 11 published and under mine showing 3900+ in which I don't have that many pages to begin with, somewhere between compressing the advanced files, emptying cache and linking up to Cloudflare everything went bonkers.

I have unhooked Cloudflare, uninstall WPMU DEV dashboard hummingbird smush pro, followed the WP 404 broken links steps with the permalinks structure no help then went advanced and followed the steps to update the .htaccess still no help.

I am on a Hostgator shared server their ultimate reseller package I only use it for this site as my primary. Normally I graduate up to a dedicated and in the past, I never had this problem so I can't help to wonder if I did something to their shared servers. or did I do something on my own.

I do not mind reloading or rewriting my pages etc. but I need the links as if you attempt to create new pages it shows /your-page-2 instead of /your-page

Lastly, I like to try and figure out what went on under the hood so I could prevent and help in the future thx. by the way, the home page is only showing semi-normal because I created a second one so it wouldn't display a soft 404 page. my site is live for my brokers and clients so I need to fix or delete everything from the server and rebuild it tonight.

http://usaap.net/