This is a crate LS3 with 1 year and 4500 miles on it. It's always had a slight vibration from 2000-2500 rpm while in gear. I took the clutch and flywheel out to inspect and found rubbing marks on the starter and outside edge of the flywheel. I took the whole clutch assembly to a machine shop to have it balanced just in case that's causing the vibration but he said this contact could be due to a bad thrust bearing. He said to use a pry bar and try prying the crank pulley forward to check for movement but I'm not comfortable doing that. Is that really the method? How hard would I have to pry on it? Car runs and drives fine.

 

You HAD a slight clearance issue there, but the parts seem to have " worn in"
I rather doubt that was the cause of your vibration issue .

 

Right on. I think I'll dremel the starter down a little more to guarantee more clearance. What about the machinist thinking my thrust bearing is the culprit?

 

There is always " some " crankshaft end play. The spec can vary WIDELY between different engine series.
I had a tattered old work truck, ( UPS delivery rig, LONG ago ) Ford 300- straight six manual transmission, was having clutch (disengagement) troubles, and the accesory belts would occasionally fall off... for " No Reason".
Old timer suggested checking crankshaft end play: prybar would easily shift the crankshaft fore and aft a fat eight inch. Thrust bearing was a face of one of the crank main bearings, and it was GONE. Engine still running, not much oil pressure,. had around 450,000 miles on it. about ready for rings and bearings I suppose.

 

I won't worry about it. I've never found metal in my oil filters and the accessory belt looks like it isn't rubbing or crooked. I'll attribute the rubbing to the starter being slightly too big in that area and shave her down a bit.

 

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..Shave it, Send it