Long post ha, so I'll summarize and say I agree with everything you said.
I just tried running it without the MAF connected. Same thing. Also had new plugs in, which didn't help sadly.
I did send Tom a datalog, and he told me to give him a call to go over some things, the first if which being a compression test. I'll call him again tomorrow. I know the SCT can dialog a lot of things, just not sure which PIDs correspond to the things I'd want to look at. Tom could certainly help there.
Mine: 2002 Focus SVT: 142k, Sonic Blue, #1654, All Options
Mods: Tom's Tune, Borla, HFC, STS, Painted Machs, Euro Grill, FRPP Springs
Hers: 2010 Focus SES: 67k, Ebony, Auto, Moon and Tune