Reuse head and bottom end bolts.

Yes.

Replace at least the exhaust valves and springs.

Depends on the condition of the valves. They either have enough material left to be ground to match the new seats or they don't. If they do, no need to replace them.

Springs are usually reusable if the new seats are installed so the valve stems come up to the correct height. Easy enough to check the spring tension and shim tighter if necessary.

Replace the camshaft and lifters.

Depends on the condition of the old cam. New lifters definitely.

Don't reuse the fiber timing gear and replace with aluminum set.

I would go with a new gear unless you know for a fact that the old one was recently replaced. For about twice the cost of a new fiber gear, you can replace both cam and crank gears with a Cloyes aluminum / steel set which will last just about forever (no advantage to using the much more expensive steel / steel set, IMHO).

He said that even though the crank journals may be OK, oversize bearings may be necessary in order to reface thrust surface on crank.

The thrust bearing width is the same for all (regardless of bearing size), and I've never had to resurface that part of the crank. It's not a factor. Rather it depends on how the crank journals polish up. If they do need to be turned, you will need to go to the next *undersize* of bearings.

His high quoted price (worse case scenario) was 1,100 dollars for:
Clean, Magnaflux, bore & hone, deck block, cam bearing install, pin fit/rod align, recon rods, grind crank, reface flywheel, balance, r&r guides, install valve seats, valve job, and surface the head. Sounded reasonable to me.

I wish my machinist charged that little.