OP, I just got back from EAS. My car put down a disappointing 349 WHP with filter, pulley, HFC, x-pipe, and rear section. My car had the oldest software version. Tom flashed it to the newest file and it put down 372 WHP.
While doing the flash, Tom showed me the plots for an '08 with 48k miles, original plugs, and old software. The owner brought it in because it failed smog. It put down 308 WHP and the plot was rough like yours because it was misfiring (no codes though). With new plugs and software, it made 345 WHP.
2008 IB E92 M3| BBS | KW | Arkym | Platte Forme A.G. | Active Autowerke | K&N | Fabspeed | Dinan | Evolve-R