So how did you have the transmission or bellhousing mounted with the aluminum bellhousing? It won't necessarily make a difference unless the mounting scheme was poor. Stock bellhousings are usually at least fair for runout, unlike aftermarket stuff. But given your problems it certainly won't hurt to measure and correct as needed. Likewise it's unusual to have parallelism problems, although it can definitely happen.
I've been playing with small block chevy's for over fifty years and this bell housing problem is new to me . In the past all you had to do was bolt one bell housing from a small block engine on to another small block . I never even heard of mis-alignment and having to use dial indicators until working on a C1. Now that I know that I have the correct cast iron and right year bell housing I'm hoping that it works .
I got the original cast iron bellhousing yesterday and found out that the one that was in there is a rare aluminum bell and will only work with a 1960 Corvette part #3764591 so apparently if it is only for 1960 , it won't work right for my 57. I don't know what the difference would be but if anyone needs one it will be for sale .
"since there were hot burn marks on one half of the flywheel and pressure plate so I took it to the machine shop and had it checked and refaced"
Check the crank flange for burrs^^^^ indicates that the flywheel is not running true. If no burrs on the crank flange indicate the crank flange. indicate the face of the flywheel when on the crank.
I had a machinist friend come over Saturday and check everything with dial indicators . He said everything is within factory specs . Put everything back together with a different original cast iron bell housing and the problem is still there . I think it is time to take a close look at the inside of the trans for possible front bearing slop on the input shaft . I'm thinking maybe it is putting side force on the clutch disc . We will see .
I think you're chasing the wrong thing. And you don't have to tear down to check. Just indicate the input shaft to the front retainer. Indicator clamped to input shaft, plunger on retainer. You may have to get creative to figure out the best way to clamp.
Unfortunately I don't have any new suggestions. My thought is it's one of the things mentioned already.