I'm certainly no expert on engines and pictures are no replacement for being able to see it in person. If the engine builder came highly recommended I would go with what they say!
If he didn't get too aggressive with the scotchbrite pads and tried to evenly work on the cylinder bores, then that should be OK.
Were all of the cylinder bores worn like that, or was it primarily where the studs pulled?
Sounds like a good plan on the heads. Replace the valve stem seals, clean the EGR passageway, and remove the head oil passageway plugs to clean (replace plugs with new ones of course). A few people here have observed oil leaks from the head plugs over the years, and they are just a couple of bucks to replace.
Ask him for documentation on the bores (diameter, taper, ovalness), final main and rod bearing clearances, piston ring gaps, etc when reassembling. You can reuse the main bolts and rod bolts no problem since they are not torque-to-yield. I would not even bother to weigh/balance the rotating assembly. Crankshaft journals are probably fine too and don't even need to be micropolished.
Two things I do recommend though and they are relatively cheap to do now. Later they are a PITA: Buy two new knock sensors (~$200) and the crankshaft/camshaft position sensor on the front head. That's the thing that dribbles black potting material after it ages. Very knowledgeable people here say it is fine to keep using, but it is relatively cheap and I want to make sure my sensors won't be able to move around for the next 10 years.
I also recommend a new TB tensioner/pulley, spring, and bolt. If your mechanic follows the service manual for TB replacement and tension, keep in mind that the tensioner spring may need a little "help." Tension should be like this: http://www.nsxprime.com/forum/showthread.php/45564-DIY-Timing-Belt-Question/page3
Lastly, you know about the harmonic crankshaft dampeners failing, right? If yours is original, I would replace with a new OEM (~$250) for peace of mind.
Dave
