What kind of RPS is it shooting? Shortened the tappet spring? Sounds like a timing issue but could be PME. Try the paper test in auto vs semi (cut out a small square of tissue paper and place it on top of the hop chamber feed tube, see if it gets blown off when shooting - if it does, you've got an air leak). Also try cycling with a weaker or discharged battery and see if the FPS loss in auto goes away (if so indicates issue is speed related; could be PME, could be tappet spring is to weak, etc)
If you've got any pictures of the open gearbox, might help us point you in the right direction
If you've got any pictures of the open gearbox, might help us point you in the right direction