Yamaha DT3. My crank doesn't have any play, spins good, but I have a feeling it is out of alignment. Before I start concocting ways to hold it so I can spin it check with dial gauges, I though I would see if there any simple ways or ideas for this. Whatever I figure out will probably be  overly complicated,

My left eye just developed a nervous tic.....



A good place to start would be a straight edge across the flywheels at 90 degrees to the crank pin.

See, that's what I mean, nothing that simple would occur to me. 

Ok, why do you think it's out of whack.
You'd get an idea just getting someone to turn it over while closely observing the flywheel if it's still in place, or the shaft but look at the taper not the thread because its more than likely someone's belted the shaft over the years & thread center countersink may not be true 'if thread is bent'
Note--flywheel may not be perfectly 100% round but will be close enough to see any shaft wobble.
Just thinking outside the square--if it's vibrating it's more likely to be loose engine mount bolts, & don't miss that bottom rear 10mm thread size one as is a bit hidden.