I just posted this up on the Google webmaster forum but will also post it here. I do believe that I got it all figured out as I stated earlier.
It was not a link, it was not content. It was a 404 error that had gbot chasing it's tail through an endless loop. The problem has been there for ever but Gbot has not been following certain things (like javascript) as aggresively as they are now.
I had 404 defined in htaccess to point to the base index page. The idea being if there is someone poking around or a bad link they end up back at the main home page.
I have a form that is several subfolders deep. When gbot read that page it found a src attribute on an input element. That src element simply pointed to home. (Please note that this contact form is the only thing on the site that was NOT hand coded by me. No excuses there, just fact..lol). Gbot troied to follow it to a page called /subfolder1/subfolder2/ home and got a 404. So htaccess told it to load /index.htm which it did. Unfortunately /index.htm tried to load js/javascriptfile.
Well, since the javascript is not at that folder level, the call 404'ed and then just repeat and repeat ad nauseum.
So, I put in a proper 404 page that does not load any other resources and redirects back to the main index page (I also did this with 403 to avoid a repeat).
Once I had that in place and tested to make sure the loop was gone I did a fetch as google and submitted just the index page for respidering.
The result was almost instantaneous. Immediately after gbot respidered my site showed back up in several rankings that it had dropped out of yesterday amd it stopped showing the warning on all except a couple of searches. Several hours later now it stopped showing the warning anywhere.
So, as I said at the top. It was not links (either spammy or phishy). It was not content (spammy, thin or duplicate). it was behavior that ticked gbot off this time.
Hopefully this helps other people experiencing the same thing to debug it.
Thanks again for all the help.
P.S. This is the result of the endless loop problem, one of the urls gbot was trying to pull, from my logs:
/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js
/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/js/javascript.js
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