@JoG and DragBikeMike

I can't thank you enough. Those pics are invaluable and the step by step description will hopefully get me through it.

I have both side covers off and a friend helped me make a tool to loosen the plug on the generator side so I can check the timing marking. I did put the piston at TDC before I re-attached the cylinder head but I did not know it was possible to lock it in position to keep it there.

I did manage to get the timing dents on the sprocket and crank shaft aligned. When I first got the timing chain in place I did so with the cam sprocket loose and when I was attaching it to the cam shaft I first put one of the bolts in just a few turns and then tried to turn the engine to get to the other bolt but something gut stuck and I could't turn it in either direction. I think I heard a small "ping" when I forced the engine backwards and I noticed the first cam sprocket bolt had  rubbed against the side of the cylinder head. I screwed in a few mor turns by hand and then everything went smooth. Is there any risk of damage to the engine?

I will give it a new go today and take more pictures as I try to follow DragBikeMike's instructions

Here is a picture of the aligned drive sprocket. I think I got this part sorted out OK.

One other question. I have read on several places to make sure I check TDC on a compression cycle. If I don't have any valves or cam shaft involved is there really a difference between compression and exhaust cycle? Isn't that determined by the cam shaft and opening of the valves? And if so - can't I just make sure the lobes of the cam shaft are both facing downwards as in the picture?

Whoah!  Kamel, you do NOT have your TDC marks lined up.  STOP, STOP, STOP.  Do not try to start.

The timing mark on the crankshaft is not paint.  It is a linear mark embossed in the end of the alternator rotor.  You are using a paint mark on the bolt, which can end up positioned just about anywhere.  You must use the linear mark stamped into the end of the alternator rotor.

You can barely see the correct mark circled in red.  It's not lined up.  You are about eighty degrees off.

Regarding your question about TDC compression vs TDC exhaust.  If you try to install the head cover with the cam set to TDC exhaust, the cam lobes will be facing up and you will be struggling trying to get the head cover on.  It will be forcing the rocker arms into the cam lobes and valves, trying to open valves.

You are correct, you want the cam lobes facing down when you go to install the head cover.  The cam lobes should be facing down and the marks on the cam should be aligned with the horizontal sealing surface.  It should look like the picture below.  Also, when correctly positioned, the dowel for the cam sprocket will be in the 1 O' clock position, as shown in my prior photo of correctly aligned cam timing marks.

That reservoir directly below the cam lobes must be filled with oil prior to starting the engine.  It can be easily filled with a pump oil can through the exhaust valve access cover.

My compliments on cleanliness.  Very nice job of keeping things spic & span.

Do you understand the caution note I last posted?  Do you now see the correct timing mark?  I don't want you to damage your engine.

Regarding pouring oil in the breather to pre-lube the top end.  The crankcase breather actually ties directly in to your bottom end.  Any oil you pour into the breather will just run straight down this cavity into the bottom end.

@DBM: Yes I think I understand where to check the TDC position. I will try it again tomorrow and veryfing wih my aluminium rod through the spark plug hole again just to make sure.

@JoG: I invested in not one but two torque wrenches. They came with calibration protocols so I think I can trust that they are fairly accurate. They cover 4-20Nm and 25-125Nm. I have never before done any mechanical work so my experience and "feel" for the correct torque is zero.