Q: Replacement engine running rough.

An engine that sounds like marbles running in a dryer is a classic description of pinging or pre-detonation, this is a sign of major engine malfunction. This in addition to the rough idle and stalling makes me wonder the quality of the used engine before it was installed. Concerning the missing engine bolts, are there clean metal bolt holes where the bolts might have used to been? This could be the sign of careless installation and may shine some light onto what is going on inside your current engine. I would suggest having a certified mechanic diagnose the problem and document everything (pictures) you might need it to prove your case later down the road. Used engines are always a gamble if you can’t verify where it came from, next time try to get a time/mileage warranty in writing to help safeguard yourself from this happening.