Diversion Engine Problem

I have a 96 XJ 600 Diversion which recently had the clutch replaced. When the garage replaced the clutch they told me that there is a design fault with these clutches and drilled some holes to allow the oil to circulate better.

Ever since the clutch replacement there is a sort of knocking/rattling coming from the engine. The noise is reduced when the clutch lever is pulled in. I have also noticed that at about 3250 rpm, the whole bike vibrates and causes the fairing to rattle substantially.

I have also noticed some minor clutch slip when setting off from stationary with a decent amount of power applied. Also gear changing does not seem quite smooth anymore.

Can anyone tell me what the problem may be. I have two suspicions, 1) thrust bearning, 2) bottom end bearing.

Are there any checks that I can do to narrow down the search?

Many thanks in advance

Robbo