Yeah CA recently went into high gear cracking down on modified cars. Any little thing these days gets you sent to the State Ref. I am glad yours was an easy fix.
I would go this route. Might as well go back to the control group and see if the maf and tune change take her back to normal. That could rule out a mechanical issue.
If you do have PFTE all around then it must be some kind of a leak. I never had any garage smell on E85 with mine. Only when i had a couple of small leaks did I ever notice garage smell. Fixed those up and nice and smell free.