Hello gentlemen I bought a manual 240d that had already undergone an engine swap. But then the engine developed a rod knock. I bought it at that point, dismantled it to confirm the rod knock, and am at the point where im buying a new engine.

I found one on craigslist that I can see run apparently so I'm going to go check it out at least.

I have the flywheel from the original manual trans. Will I need to buy the flywheel (flex plate?) or anything from the donor engine's auto trans? So I can ensure the flywheel I have matches the balance of the original flywheel?

I am a noob, thanks for the advice!

Yes, get the flywheel & flexplate (two separate pieces on earlier engines) with the donor engine. Ensure that they remain on the crankshaft, or match-mark them to the crankshaft for position if there is a need to remove them for transport of the engine.
The imbalance of the donor engine flywheel is to be replicated in the replacement (manual) flywheel.

the donor engine is from a 1984 SD so the flex plate is one piece?

A bit of a mea culpa is in order here; all 617s should have the two piece flywheel/flexplate.
One piece with 60x engines, aka "later".