Engine was cranked correctly all the time (so clockwise) and marks line up perfectly (cam alignment) both before and after the belt swap and I just checked the new vs old belt, and they are exactly the same size, so belt stretch doesn’t explain the difference. Lastly, with the crank mark off by the 30 degrees or so I indicated, piston #1 was at TDC. I checked my marks many times before removing the old belt and reinstalling the new one. The old belt looked as good as the new one, as many have said on ST-Owners in the past.
I think the last thing I’ll do before final assembly is place the carbs back, fire the motor (very briefly), make sure it runs nice and smooth, shut it down, and then reinstall the TB cover, radiator, etc. I’m very sure at this time it’ll run fine since the marks were the same pre and post belt replacement. Very strange and rather unexplainable, but it is what it is.
I think if I set everything according to the manual, I might actually mess everything up and as it is now, the engine rotates nice and smooth without any parts colliding- if I set it the proper specs in the manual, piston 1 will before TDC and I risk wrecking the engine. As I’ve said, I’ve checked this at least 10 times before taking the old belt off and the belt was not at all stretched.
Hopefully when I do this work on the 2000 ST, all will be as expected/ normal- that bike I’ve owned since new and the TB has not been changed, so it should be as ‘factory sealed’.
EDIT: Here’s something interesting and I didn’t notice it until after I used the starter with the engine in the ‘no run’ position (on the 94, you can still spin the starter in the no run position- can’t do that on the 2000). Anyway, the crank bolt when turning is normal but the plate directly behind it but in front of the sprocket spins very slightly eccentrically- to me, this means someone was in there before and probably messed up the crank mark cover/ sprocket cap. Since I have everything set properly and it’s difficult to break the crank bolt free, I’m just going to leave it as is- what I may do is fire the engine after carb reinstallation (just for a few seconds) to make sure it starts/ runs properly, then reinstall everything- sounds OK to do that I assume. I don’t foresee myself ever changing the belt on the 94 again- I probably won’t put another 90K miles on it in my lifetime or will sell it by the time a new belt is required