I have been chasing similar issues myself. I also think it is in the tune.
I've done some testing with MHD v7.1 e60 and v6.1 e40 maps and can recreate the issue quite easily with either map.
With the car in M4, if I tip into the throttle (roughly 30-40% pedal input) at 1500RPM and log out through 3500RPM I see similar throttle closures and other roughness in the logs and feel significant chop in the 2500-3000 range.
The car has fresh plugs, Eldor coils, index 12 injectors, new turbos, etc - it is well maintained and has 55k miles. No codes are being thrown.
As examples:
http://www.datazap.me/u/mwahlert/log...-31&zoom=26-70
http://www.datazap.me/u/mwahlert/log....83&tmax=62.60
I gathered some new logs yesterday with a smaller number of channels so the resolution seems to be higher. I'll upload them later.
WOT logs are clean.
http://www.datazap.me/u/mwahlert/log....80&tmax=99.60