How sure are you on the sleeve measurement? Usually the problem is the sleeves sink into the block requiring the counterbores to be recut. Originally, there was a special tool the dealers had to cut the bores and a .020 thicker sleeve. The thicker sleeve is no longer available. Now you either have to have shims made, bores re cut and the block surfaced, or have the counterbores re sleeved.
If your measurements are correct and the sleeves set that high, it sounds like the block was surfaced and the counter bores not re cut.
When re cutting the bores, you also need to pay attention to the piston protrusion. The original blue prints call for .002 to .029 above the deck. My machine shop says his book shows .040 above the deck. Surfacing the block can quickly bump up piston height too far and the pistons can hit the head. My D17D project went from a simple head gasket job to a complete overhaul due to the pistons hitting the head and the sleeves too low in the block. In my case, a compressed head gasket was .055 and the pistons were near .060 above.
You need to pull the engine to tear down and decide if the counterbores are good enough to recut. Mine weren't due to rust and cracks around the head bolts. In my case a replacement block was the cheaper and better repair.
To give an idea what I've gone through, I have right about $1000 in the new block. $500 for the block, $200 for hot tanking and line boring the mains, another $200 to recut the counter bores and surface the deck, and about $100 to put new cam bearings in it. The total overhaul not counting my labor will be between $4K and $5K. I'm leaving nothing to chance though.
The problems you have are NOT going to be inexpensive to fix. Private message me if you have more questions.
------------- "Any man who thinks he can be happy and prosperous by letting the government take care of him better take a closer look at the American Indian." Henry Ford
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