Valve clearance correct or not

As the tip of the valve gets hammered from a flat surface into a dish (!) it becomes increasingly hard to obtain a true clearance using feelers. Best off by using an alternative method. Pitch of adjuster screw thread is 1mm so one turn of the adjuster screw is 1mm. You want 36degrees (one tenth of a turn) for the inlet and 54 degrees (one and a half tenths of a turn) on the exhaust. 

I use the Kedo flat ball (elephant foot) adjusters and devised a plate with 36 and 54 degrees marked on it to make the adjustment. You can only use the flat ball adjusters though, if the tips of your valves are still fairly flat. Yours sound as if they've been dented.

Valves are checked at TDC on the compression stroke. Left side (generator) engine cover off. Use the pointer on the engine block and the TDC marker on the flywheel. Always rotate in the direction of engine rotation to arrive at TDC. If you go slightly past it, keep going all the way round to get there again. Never wind it backwards.

To inspect your valve adjuster screws and tips of the valves, remove the adjuster screws for inspection of the surface that bears on the valve tip. Take great care not to let them fall into the motor!!! 

They tend to get chipped around the edge and develop a flat spot when worn. Next, take a peek at the valve tips. You'll be able to see them with a dentist mirror and flashlight once the adjuster screws are out. It should be possible to get an idea of how bashed in they are. (High mileage bike? They'll definitely be bashed in.) 

I made a degree plate with zero, 36 and 54 marked on it. It has a hole at the centre of the radius to pass the adjuster tool through. Line it up with zero and wind out to 36 or 54 and snug down the locknut. You'll get the feel of 0.1 and 0.15mm quite well after a few goes! 

If you try and check it afterwards with a feeler, the chances are you won't be able to get the feeler in there!

Thanks for all that. Definitely will do that.

Sorry to hear you've got wider issues regarding the head cover! Your options are likely to be Haynes or Clymer as far as manuals go. Both should have comprehensive step by step for engine stripdown and refurb as well as routine periodic maintenance and spec/tolerances etc, I know the Haynes does.

You're right that the cover is not listed except as an integral part of the whole cylinder head assembly. Reckon you're looking for a used engine to strip for parts! I shall make a prediction: A weekend touring breakers yards lies in your future!

This is definitely an engine out of frame job, I'm sorry to say. Glad you're already eyeing up some suitable parts on the bay. 
Once you have a manual you'll see the process for replacing valves. Never had to on my current machine but is pretty standard if you have the new parts to hand and are confident with the fine details like lapping the valve seats.

Gasket sets become important. Athena and Yam are recommended. Issues with incorrect thickness of important parts in off brand gasket sets. The head cover needs Yama bond number 4 or similar to create seal with head. It'll all be in the manual.