I've been hacked, permalinks are going off site

It started about a two weeks ago when I opened up comments to non-registered users. After awhile, getting comment spams, I put some Captchas in place.

I was monitoring my traffic very closely and I kept noticing traffic from ubiquity services. The ip’s kept rotating, the user agent and other headers kept rotating. In essence, it was not consistent with a human.

I began blocking those ip’s on the htaccess level. I also contacted ubiquity who essentially said, “not their problem”.

I stopped getting as much traffic from ubiquity but noticed very odd referral urls. I was getting referrals from a lot of non-search engines, and when I visited their sites, there was no trace of my domain. I knew something was up.

I looked into various things to shore up my security even more, many of which ended up breaking my site, or locking ME out.

I scanned through my folders looking for modified dates. I ran a few WP plugins on security that exposed certain “base64” codes etc. But it all looked like it was a normal part of the plugins in question. (Adminer has a lot of that.)

Last night when I checked on my site, and clicked on one of my permalinks, it took me off site. I discovered ALL of my links are doing that.

I removed EVERY file from my WP directory and put a clean install of WP. I also downloaded my plugins a new. It did not fix the problem which leads me to believe it may be part of the database, which is not my strong suit.

I’m not sure where to look and how to troubleshoot at this point.

I need some help.