I smell something fishy. Unless the old thrust bearing was toasted and torn up pretty bad there is no way to go from .010 to .003. NO WAY. Something is wrong here. I would like to see the parts. Sounds like BS to me. Major BS. I would really like to see how he measured the end play.
At my shop I would charge 3.5 hours to change the main bearings and rear main seal and 2.5 to do the intake gasket with cleaning all the parts adjustments. That is @ 60.00 per hour plus parts. Main bearings are 30.00, rear main seal 7.00, pan gasket 15.00, silicone for main cap and intake 4.00, 2 cans of brake cleaner @ 2.00 per can, Intake gasket 27.00. oil 12.00, filter 5.00.
360.00 labor
104.00 parts
464.00 total and maybe a discount for a TR guy
I still think this is TOTAL BS the story your being told unless I could see the parts taken out and the parts used.