I've been guilty of aligning one of my custom HDs this way. Turns out the frame was bent at the pivot point and no matter how many times I measured -the belt would not track at all. Didn't find this out until I dissasembled the rear end of the bike. Turns out there were 2 problems; the swingarm shims were too narrow and when the pivot bolt was tightened it pulled in one side of the frame, and the wheel didn't have the correct spacing. Between the 2 the only way to track the belt (which was chirping like a flock of birds) was to align it much like you described.
It's good deductive reasoning on your part, it's just not the most accurate way to accomplish proper wheel&belt alingment. BTW, I'm not a mechanic "perse" but having owned that bike I quickly learned enough through bad experiences to muttle my way through most anything the Warrior can toss in my direction.
Sounds like you're on the right path too. [

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