Lower end vibration

My new motor is experiencing a bad vibration that start around 3000 rpm and quits around 3500,it shows up on accelaration,and deaccelaration.It sounds like it coming from the tranny part of the cases,you can hear it well around the breater cover,clutch cover,and the kickstart block off plate.I had my tranny undercut,clutch basket backing plate rebuilt,and I have removed the kickstarter,any ideas?

Thanx in advance!

What kind of bike?

KZ900,ltd

Who did the undercut ?

R&D,I strongly believe that its in the clutch basket,had it rebuilt and I think its out of balance,tranny feels good,Im going to take a look at the clutch itself tomorrow,and if it checks out,Im gonna go with it,I'll pull the basket back out next winter.Thanx for the repliesB)