the engine diagnosis game!

moper said

I would run a bottoming tap down the head bolt holes. It sounds like they are flat enough. But you may want to shorten the bolts gently (dont let them get too hot) by about 1 thread. They may be bottoming in a hole or two due to milling. I've only seen that once, but something looks fishy. Does the intake fit well? The bolt holes are centered in the holes?

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You need to use a thread chaser, not a tap. A thread chaser cleans the threads without cutting metal like a tap will.
You can make a chaser out of an old head bolt. Get a dremel tool with a thin flat wheel and cut three or four grooves, length-ways, around the diameter of the bolt. Then, clean the bolt threads with a wire brush to knock off any burrs. The grooves collect any gunk that is on the threads of the holes.
After that, spray a little WD-40 on your new thread chaser and run it down each bolt hole.