Gen 3 Prius sounds terrible after replacing headgasket

So for background, bought a prius off of a friend. It has about 250K miles and the cylinder 2 was misfiring because of a head gasket leak. I got it cheap and figured this would be a good learning opportunity. The second it started misfiring, she had stopped driving it. I tore the engine down and checked the head and block for flatness, the depth of the 4 pistons for a bent rod. Everything was good. Installed a FEL-PRO gasket with new seals and put everything back together. Messed up the timing the first time (off by a tooth because the tensioner hadn't engaged) so redid that yesterday. Installed new spark plugs as well and cleaned out the intake and EGR as well since I was in there.

Anyways, when I started it up for the first time, the engine (almost violently) shook before quickly settling down. I saw that I was getting a misfire on cylinder 3. Swapped out the coil packs and was still getting a misfire on 3 (and now also 1). Still sounded bad each time I turned it on and it kept throwing misfire codes. I swapped to the old spark plugs and weirdly enough, no more misfires. The engine doesn't sound as bad either, but it's still not great. It shakes and even when it calms down, I'm getting this fluttering sound which I feel might be an exhaust issue?

The very first time I started the car after replacing the head gasket, the engine was shaking back and forth so hard that I think it did something to the exhaust, I could see a small amount of exhaust leaking from the back of the engine so not sure if now I have two problems.

Unfortunately can't post links directly on here yet but have some videos that illustrate the sounds.