1965 289 2 barrel rebuild question

I would say keep the original, if you have the space.
You can buy a running car with a 5.0 and transmission pretty cheap these days.

You need to get the date codes to tell if it's close to being the original engine. The date code is the number/letter/number combo next to the casting numbers on the engine block. They look like they're cast into a tag with two screw heads. First number is the day of the month, the letter is the month code, starts with "A" for January thru "M" for December, skipping the letter "I". The last number or numbers is the day of the month it was made. This code should decipher out to a few days to a month before your car was built. This same date code is also found on the heads, under the valve covers, next to the valve cover rail. Usually hidden by built up gunk. As long as these codes are dated before your car was built, you can safely consider it to be the original engine.

If that engine tag was still on it, I'd say it's a good bet the rest is original. Little stuff like that usually gets left off in engine swaps.