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OP. Get some actual data. ISTA has a nice misfire screen that you can easily help identify misfire and the cause (good guess, or maybe a better route to go down).
Taking off the plenum will do nothing barring the intake temp sensor as this engine is a SPEED DENSITY calculated--no MAF in intake.
I would also try resetting all adaptions in the DME. I'm not sure about your tune, but it could have an effect on the running operations and the DME calculations.
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2008 BMW M3 E93 MT, 3.15 FDR
R135
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