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: 2004 Subaru WRX Wagon: 116k, WRB
Gone: 2002 SVT, #1654
Hers: 2012 Focus Ti Sedan: 67k, SGM, Manual