Throttle bodies out of sync comes to mind.
Check everything is fix and fine, if so you need to balance (sync) them.
I just experienced an 1198 with TB nut for rear cyl loose just a bit, it ran awful on low openings.
And a huge AFR difference between cylinders, so I stopped there and found the linkage was loose, fixed that and tadaa!
On 998 also check that TB opens fully, Ive done a few and on those they didnt, not even close, if so grind the stop to fit.
Cam timing and that gave 5-7 hp all the way from 6k up, silly