Posting this to help others who may stumble upon this.
Took my bike into a local coopco-op, armed with my roommate's hunch about the freehub body, and I removed it, and the guys there said that it had too much play and wasn't ratcheting correctly. Either damage to the pawls or gunk.
Put a new freehub on, and it's as good as new. The take away here for me was: if you're able to stand up on your pedals while going up hill no problem, and your chain only feels like it's skipping after the freehub disengages (coasting) and then reengages (starting pedaling again), it's probably not the chain or cassette/chainrings.
I think this is a weird problem since I had brand new gears and chain, but a very old freehub, which I doubt happens too often, but this worked for me, for what it's worth