Low power and bogging down at high RPMs, you say? sounds like you raised the pressure by filling in all of the holes and now it's blowing straight through your exhaust (is it leaking gas or smoking alot?) Perhaps try removing the material you filled the stock holes with? See how that runs? I know its a huge pain dealing with testing the crank, having to do complete teardown after teardown is a huge hassle, but to get maximum performance, it's a must. Do you have reed valves by chance? another way to lower your transfer pressures is to add the boost port (you NEED reeds to do this).
Also bogging down is an ambiguous term, does it four-stroke? or does it just randomly lose power at high RPMs? Does it make any peculiar sounds, such as sounding like its drowning? Are you using the stock CDI? Are you sure you're not going beyond your previous top speed (aka higher RPM than before)?
Side note: How did it affect the vibrations? My understanding is people on this forum drilled the opposite side of the crank to counter balance it (though all the pics I saw used 3-piece cranks so the removed material is hidden).
