Jen, I wish I knew what to say to make all of this go away. I don't recall how old Mr. Meow is but I hope this might help just a little bit. When it came time to have Groucho neutered our vet did the standard pre-op tests. He tested positive for FIP but our vet said that since he was under 6 months old he could be testing positive for his mother's antibodies. Doctor scheduled a second test a few weeks later, the count was better but not where she wanted to see it. A third test was done and Groucho tested negative. This might be something to discuss with your vet.
Many prayers continue to be prayed for Mr. Meow and for you.....