Aye leah,
I am sorry for the delay in replying and my thanks to SteveL for stepping into the breach.
"Just to make sure I've got my 4 stroke cycles right, the compression stroke is the upward one compressing the fuel/air that came in on the intake stroke. Therefore on this stroke all valves closed right?"
YES"If 180° out some valves would be open & you wouldn't be able to check the
open valve's clearances as there wouldn't be any?"
YESIf the cam/valve timing is out by 180deg, the valves won't touch the piston, but the spark will arrive with no compression on the inlet or exhaust stroke!
As SteveL says "if the timing is out by a tooth or 2 on the camwheel, then you'll feel the piston touch the valves........"
But I don't think that is your problem or else the engine wouldn't have turned over/ you'd 'ave heard a 'dink', as valves touched piston!
Before you strip bits of engine cover off, are you sure that the electrickery bits are all 100%?
? I will send the 'Ignition' section from the Yamaha workshop manual, by mail attachment, for you to use.
Sorry not to be of more help and I hope others will help if they can. Or 'SHOUT' if I have made an error!
My regards, Bill.