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I would think the vibration would get progressivly worse as the RPM's increased, if it was crank runout. Which would lead me to believe it's either your IPB (back to that), a trap door bearing (highly unlikely), the Main Drive Gear needle bearings (pretty likely), since you've ruled out the big bearing. Or any of the needle bearings in the trans gears.
Is it gear specific?
It's most noticable in 6th, because that's where I'm at most of the time (when on a slab). But still there in 5th and 4th, only @ higher frequencies while maintaining the same mph as 6th. I don't know if I noticed it in 1st thru 3rd.
Since it's not gear specific, you can probably rule out the trans gear bearings.
I'd still be leary of the main drive gear needle bearings and the IPB though.
You never said why the seal went bad and why they replaced the inner race?
Did the race walk on the output shaft? A good sign of a bad bearing is usually a bad seal.
Anyway you look at it - it was a shoddy job to only replace the race. Especially since you can't really tell if that's your problem now, without taking it apart again?
The servicing dealer said the IPB race was "worn down", but the IPB was ok. They said the extra radial clearance could allow more shaft/seal deflection resulting in a leak path. I think it would be more likely that the leak could've resulted from the race walking out of place. But what do I know; I wasn't there to see it, nor did I see the removed race.
Before they took in in for service, the serv. mgr. said the drive belt felt tight, but this check was w/ his finger on a machine that wasn't completely cool. I was ready for that comment, and told him it was set @ 7/16" on some random point of the belt (not necessarily the loosest part, as per the shop manual), so it's nowhere near overtightened per the shop manual. Anyway, I told them I'd keep the tension that they set after reassembly. I just checked it and it's @ 1/2" to 9/16", so it's a little less than spec. I'll keep it there as I don't think it'll jump a tooth.
I agree that the needle bearings could be suspect too. If the IPB race was the cause of the leak, and the IPB was the cause of the race wear (or walk?), I'm hoping the leak will show up again before mid April when my factory warranty runs out. I'm probably only gonna get another 3k on it till then.
Update,
Looking over my work order billing list, it appears that the servicing dealer DID in fact change the IPB roller bearing (p/n 9231) when they changed the oil seal p/n 12052A and inner bearing race (p/n 34091-08). My bad. I should've looked closer @ the w/o and just not taken the service consultant's word (before typing on previous posts). A phone call to him today confirmed that the IPB was done, but he was just not aware of it when I picked up the bike. So for now I'm gonna rule out the IPB as a vibe cause.
I was also concerned that the w/o had only 1 qt. (32 oz.) of primary oil on it, when the manual states 45 oz. refill w/ primary case removal (and 38 oz. for drain-and-fill). He confirmed the w/o stating "they only hold a qt.", so now I'm gonna pull the cover and look in there, but I'm not sure how to tell if it's 13 oz. low, as there's no oil lever diagram for clutch pack submersion level in the manual. Any Ideas?
Also tried to corner the service consultant about the vibe issues (since we've rulled out the IPB and compensator), and he said the motor mounts, most likely. I don't think so. Looking more like the trans input needle bearing (s), but unless these things explode, I guess I'm never gonna find out. :-(
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