I'm not really sure what to tell ya. One thou should not normally cause problems, so if the machine shop figures it will work, probably it will. I haven't taken a 3B apart, but all other engines I've worked on with liners had the liners protrude slightly above the block surface (Alfa's and...
Although I agree with Woody, in most diesels you don't have that much room between the valves and the piston. If you do end up surfacing either the block or the head or both, you may want to make sure tolerances are still sufficient. If the deck isn't too bad I would just clean it up with a...