Engine / gearbox screaming HELP!!

[Tripnut]

My brother bought a CBX unseen from a guy down south, on the first ride about 3 miles out the engine seized at 70mph on a dual carriage way (scary). A subsequent strip down confirmed that the strainer was blocked and had starved the engine, every bearing was shot so my brother bought another CBX with the intention of using the engine from bike 2 in the bike with the very dead engine. Due to time etc he decided he wouldn't end up rebuilding the bike so I bought the two bikes from him. I got a rebuilt engine off Ebay (mistake!!) the rebuilt engine seemed OK, a look down the plug holes confirmed that the pistons looked new and when I took the clutch cover off to replace the painted one for a nicely polished cover the old cover looked new inside.

Alarm bells rang when I tried to time the ignition, the lobe was 180° out so I had to rebuild the ignition stator to suit (not the biggest hassle) and I thought that it was an easy mistake for the engine builder to make when you look at the manual which shows two positions for the lobe! The engine ran perfectly once the carbs had filled up (result )

Now to the interesting bit: I took the bike for it's MOT the other day and got right to the gates when I heard a terrible noise coming from the back of the engine. I switched off and let it cool, restarted and it made the same terrible noise which sounded like a dry bearing or the clutch rubbing on the case. I have just taken the cover off the clutch and all seems ok.

Update 1
On taking the clutch center nut off I see that the Belville washer is missing and the clutch wont slide off easily like the one I had when I was 18 so looks like I need to find a puller that will fit or make one (not going to be easy because space is tight). Good job I now seem to be the owner of 4 engines so I have lots of spare engine parts!

Any ideas?