On a RT2 and DT2 the cylinder head, the spark plugs holes enter at an angle.  For setting the timing, how do you find TDC when the timing tool requires the plug hole to be directly over the center of the piston for accurate measurement?  

Great question!  A lot of people don't even think about things like that.  

Yamaha Factory Service Manual in the Tech Library has the answer.  

(Hint: The answer has the words "pull" and "head" in it.) 

Personally I just get a small screwdriver, nail or wire & get it as vertical as I can down the hole & rock it slowly back n forth over TDC then- go- right--THERE. Then mark the flywheel with something visible like white twink & mark the case at the sane time. Can mark it anywhere on the flywheel & case that's convenient for you. The reference mark you could reliably use in the future so long as the flywheel key hasn't been damaged. Another way is "off with its head" & mount a dial gauge over the piston then rock backwards n forwards to get it close then zero out the gauge then re-check & move the dial if need be so rocks over at zero at its highest point. I'm waffling on & over complicating things as usual sorry.

Thanks for the