Update on my 250X:
The intake valves had 0.000" clearance with 1.600mm shims and wouldn't start. I ordered the two closest sizes that RMATV had in stock (1.450 & 1.400).
I popped the 1.45s in there released the tensioner, rotated the engine by hand a few times and remeasured... still 0.000" on the intakes. Pulled it apart got the 1.40s in there, same deal, measured and got 0.102mm (spec is 0.120mm (+/- 0.030mm) so the target is between 0.150mm and 0.090mm). That's on the tighter side but I don't have any thinner shims so it'll have to do for now.
I put it all back together and sat back just staring at it wondering if I'd forgotten anything important. After a few minutes I was satisfied that I'd done my best and figured it was time to put some gas in the tank and give it a try. I've never dug into a bike this far and was full of doubt and question. When I hit the starter was it going to sound like a coffee can full of marbles? Maybe nothing would happen at all. Maybe I'd be right back where I started and just crank and crank with no fire. I twisted the throttle three times, pulled in the clutch, hit the starter and almost instantly it fired right up!
I warmed it up and checked for leaks then rode it around for about an hour. I'm going to put a few more hours on it and then check the intake valve clearance and see how much, if any, deviation there is and decide where to go from there.