Ok so from your reply and a thread I found posted ages ago on this site....
I see why I'm second guessing and seem confused, I listened to a friend who's a car mechanic told me that No1 piston is closest to the cam chain /clutch side. And the 2nd piston is what the manual refers to needs to be at TDC.
Which is why I said that on the 2nd piston (flywheel side) at TDC its showing at 1F and not 2T....
The post I read said that the second piston is actually on the right not left, when sitting on the bike normally.
So.... in actual fact the lower end is sitting correct at 2T on piston 2?
Whatever I took out did go back the same way the woodruff-key was exciting, but I didn't end up having any spare parts left over
every nut n bolt accounted.