Clutch wont engage - 2003 Yamaha YZ 125

Check there is free play at the clutch slave cylinder , if the cv joint or drive shaft is broken it should make a noise when in gear with clutch engaged .

So if you raise the revs to say about 4000 rpm and let the clutch out does it stall or judder or both will it engage at all and pull away ?

The gear box should be okay. Check the clutch-watch if the clutch fork on the bell housing moves when someone presses the clutch. If it doesn't move, the cable needs adjusting, or if hydraulic clutch diagnose the clutch master and slave cylinders. Either one should cause the clutch fork to move and engage the clutch.

do you mean disengage? check for a bent clutch fork, good luck.

It seems you have a throw out bearing at fault, got to dis connect the transmission for that one

Does the clutch not engage( ie it slips & wont pull away) or does it not dis-engage (ie always in gear)
Was the clutch dismantled or disturbed when top-end was replaced
Is clutch hydraulic or not

if the clutch wont engage it probably needs replaced. clutches have lining on them, when the lining wears out the clutch wont engage

The car won't move with it in gear and the clutch pedal out?

if you lost tension on chain and now it wont turn you might want to check sprocket