IMO, I'd use all the stock bolts, TTY works, and they're pretty proven from the factory.
When I assemble engines, I use Lubriplate on everything minus the pistons. Those along with the wristpins get motor oil. Get a good angle meter, and make sure all of your TTY settings are spot on. A good wrench and socket set with no play is key.
You're heads probably have cracks, but they're likely ok. As long as the valve seats are still in tact, you should be good there. Have the crank polished, install new bearings etc.
One thing to note, if you replace the cam bearings, make sure that the shop has a cam so that they can true them up. I didn't do this when I had redone mine, and it was a lot of sanding, measuring, and it was a true PITA.
Above all else, cleanliness is godliness. Keep things wrapped up until the moment you're ready to put it in, then clean, check, clean again and install. If you're going to leave the shortblock assembled on a stand for any length of time, spray the bare metal parts down with oil, and cover it with plastic taping the ends shut.
