Originally Posted by sweller

There are two marks - one is behind the small cover on clutch side. NUMBER 2
There is mark on the clutch basket which lines up with a mark in the case when the engine is at TDC.

The other is larger and at the top of the engine and is retained by two 8mm hex head bolts and shows the cam sprocket. NUMBER 1
There is a mark on sprocket which lines up with a pointer cast into case when the engine is on its compression stroke (valves closed).

Another useful cover is in the centre of the clutch cover and exposes a hex head that allows you to to turn the engine. NUMBER 3

If you have an Adventure Spec Bashplate you'll need to drop the front of the bashplate to access the covers - especially the centre engine turning nut.

See here for numbers: