Are you sure you're on the right TDC? (I know you said you were) Putting my engine back together and getting it tuned on the first go I had #4 at TDC based on the T 1-4 on the plate. Set the clearances for 1 based on that and everything was out of whack (lot of slop on the rest) until I realized what was going on. 180 degrees around and everything popped into place as far as the valves being adjustable as expected from the manual.
I don't think you can be too off when sticking the gauge in there if you can see the valve and the adjuster you're in the right spot (based on my VERY limited experience).
BTW, for all the folks who've done this a few thousand times, how can you tell other than looking at the cam and puzzling out what's about to hit (probably not doable with the engine in frame).
Start with #1 and from the right end of the crank turn it clockwise- let the intake valve open then close then watch for the "T" 1-4 mark on the advance mechanism to align with the pointer on the crankcase. #1 will then be on compression stroke
Is giving it a run around the crank the only way to know for sure?
A noob wants to know
Iggy