I have never 'cut' a cdi, so can't help with that. It's seems a popular mod.
Sounds like your engine is 'four-stroking' at wot.
Main jet is too rich, causing it to overload with fuel and only fire every other stroke.
You will need to replace the main jet with a larger number, (probably +3 or +4 from what you presently have), which will be a smaller hole in the jet.
Of course, timing and condition of the air filter should be checked, first.
redk