I havnt read all the posts but ill put my say in.

If your replacing head and/or base gaskets, they will only go one way so you cant get it wrong. DO NOT use goo or gasket paste here. It simply is not nessessary and leads to problems.

Ensure the mating surfaces are immaculately clean and all the old gasket is removed. It can be a pain so use a blunt razor blade to remove any baked on old gasket. BE VERY CAREFUL not to nick or put notches in the mating surfaces.

For the rocker cover, you can use expensive yam bond or any other high temp gasket sealant. Its not under high pressure and a cheaper gasket paste will surfice.

For alternator and clutch covers, use the Yamaha paper gaskets. Again, no goo or paste is required.

To set the timing, remove the 2 caps from the left hand side alternator cover. Rotate the alternator with a socket until the timing mark is at TDC.

TDC on the rotor can either mean the piston is at TDC or BDC. You need to ensure the piston is at the TOP of the barrel. Put a long screw driver etc down the spark plug hole to feel where the piston is.

When you are sure the rotor and piston are in TDC position, line up the cam shaft so all the valves are closed and put the camshaft gear on with the two timing lines horizontal to the head.

Cam chain tensioner goes in last. Once you install the tensioner, make sure all the lines mark up again.

Turn over the engine by hand a few times to make sure all is well..

P.S Buy a QUALITY torque wrench and use it !!!!

If you need anymore help im happy for you to PM me. Im a qualified Motorcycle Mechanic !

__________________
Did some trips.
Rode some bikes.
Fix them for a living.
Can't say anymore.