WARPED HEAD ON A Y485T engine

You can take lead readings to determine the actual clearance between valves and piston, and head and piston, then you can determine how much material you can safely remove. It your post you are using the numbers one-and one-half thousandths of an inch and two-and-one-half-thousandths of an inch. That's not very much at all. If the machine shop used an accurate straight-edge, they could determine easily enough how much material to remove safely with a feeler gauge. I would try a different machine shop, their lack of knowledge kinda scares me. Usually a 0.005″ to 0.015″ cut is sufficient to eliminate any warpage without issues. 

Also, when tightening the head, do it in two stages following the sequence each time. First, torque to 75% of the full value. Second, torque to 100% of full value. Make sure all threads are clean.

chances it is ok but when you have a minute use a straight edge on the block. I have seen raised places around the bolt holes. Was this engine overheated?

If your pistons have machined “eyebrows” in them, then I would do a lead check to be sure.

Do the first stage torque to 55 lb ft, then second stage to 112 lb ft.

They didn't shave much off the head (0,010) so it couldn't have been that bad.

Good luck.

it will not take to much more time but I like doing a three step torque like 40 75 112 but that is just me.

A little late for a reply, but I replaced the head gasket on my 485 several years ago and did the 2 stage ramp up torque tightening.  have put around 300 hours on the tractor since with no problems.  Wouldn’t hurt to go to 3 stages as Dave suggests-purpose of the exercise is to make sure the pressure on the gasket is about the same over the entire sealing surface.