I have been doing the same thing with my 1987 Phizzer. RPM's are low, only 5500-6000 rpm's. Manual says 6300-7000 shift rpms. First I found a scored piston, replaced that, then went through my chaincase and bearings, OK. I have found some kinda drag where the track drive sprockets meet up with the track. I may have a bent drive shaft. I also had the front springs @ the stiffest setting and backed them off to the softest to take pressure off the slides. I do have the graphite slippery slides, but they don't seem to help.
I tried a new spring on the secondary, but it didn't help. I havent' gone throught the primary sheave yet. Engagement rpm is fine, around 3k's.
Anyone out there have the Yamaha factory manual? I REALLY want to know what the A,B,C and 1,2,3,4 settings on the secondary are supposed to do in the grand scheme of things. I really need to get my rpm's over 6k on top.