Help!?! Just took apart my 360, and found bad things!

So what's your budget?

Since the engine is out anyhow, I would completely disassemble it and give everything a cleaning, measurement and visual inspection. Unless I saw something that scared me, my plan of attack would be something like this:

Heads: Take to machine shop, probably need new guides, resurface valves and seats, springs to match cam.

Pistons/Bores: Clean piston crowns and ring grooves, hone bores, new rings same size.

Bottom end: Replace bearing inserts with same size, polish crank.

New: Timing set, gasket set, cam & lifters.

This would be an "Overhaul" not a "Rebuild" which will be fine for freshening an otherwise healthy engine. Obviously if the bores are out of spec, or there are parts which are damaged, you'll have to dig a bit deeper.