So the bolts are bottoming out?
If it's the factory 6.0 bolts, and was in front of an auto, it most likely had a flex plate spacer that's .4 thick

I had a nv3500 5 speed behind a 4.8 and used the factory bolts. Also used the same bolts for ls1 style flex plate and 4l80e behind the 4.8, and now the same flex plate and bolts behind a ls1.

I'm guessing you have the long bolts for a 6.0 with automatic.