I think that the easiest possible way to handle this would be to study vegan recipes. Try making the ones that sound good to you (omit any soy/processed ingredients) and add fat/meat to each dish. It will require some trial and error for sure - but who knows, maybe YOU'LL have the first recipe blog covering the subject. There are some pretty fantastic vegan recipes out there that are simply CRYING out for bacon. ;)
Hey...I also found a lady who is starting to eat paleo with autoimmune modifications and is blogging about it. She's taking part in a study as well. I'm looking forward to reading her future blog posts.
Her December 13, 2010 post discusses some sites she suggests for recipes and talks about her modifications to the paleo diet.
you may find that even standard paleo eating helps your autoimmune symptoms a lot. this has been the case for my wife. further improvement is clearly possible but she's already feeling notably better than she had been just a few months back.