0301 code and no power after 0331 swap

So awhile back my 01's 0331 head cracked. Lovely. Had a spare engine from a 96 laying around so I used that head. Never had any issue with that 96 engine. Used an adapter plate to mate the 01 exhaust system to the 96 head. Everything seemed to go smoothly. I drove the Jeep back and forth to work for a week with a nice mix of highway and backroad driving. Logged just over 150 miles without any issue. The Jeep drove and felt great from idle up to highway speed. The whole time though the temp was over 40 outside.
Then just the other morning when it was down below freezing, when I fired it up there was a very noticeable exhaust leak. With a 96 gasket, adapter, and 01 gasket between the head and header, I'm not too surprised. Anway - as soon as the Jeep warmed up the exahust leak went away. I thought, great, I'll just need to tighten up some bolts and be good to go... well, when I got on it while getting onto the highway (now Jeep's up to temp), my check engine light started flashing at me and then stayed on. Then it got very sluggish and when I got off the highway it idled really rough and felt like it was going to stall. When I left work, the Jeep fired up just fine, sounded fine, idled fine, didn't seem like anything was wrong except the check engine light was still on.
Drove the little bit of backroads from work to the highway with no problem, pulled a long hill on the highway without any issues but a little further down the road, once the Jeep warmed up though, it felt really sluggish again and ran like crap. When I got it off the highway again it started kicking and missing really bad and had no power. Really surprised it didn't die on me before I limped it home. No signs of leaks or smoke or anything weird. Parked it at home, checked the oil and the radiator and no signs of mixing fluids so hopefully that counts out a head gasket issue. I put a reader on it and pulled an 0301 code (cylinder #1 miss). So doing a little searching on here about it looks like it could be a huge number of things so hopefully someone can help me narrow down these issues.
So the fact that it runs fine while cold but runs like crap when warm and the fact that I have an exhaust leak really makes me think it's an O2 sensor. Seems odd that this would happen right after the head swap which leads me to believe the exhaust leak lead to a potential O2 sensor failure. I think that's going to be my first fix, replace those. Thoughts?
Is there signs of something that I am missing that would lead to something more serious like a PCM or anything else?

Just trying to prepare myself for the long task of trial and error tracking this issue down.
Thanks in advance.

Common sense should lead one to consider that the problem is related to your recent repairs. Find and fix the exhaust leak. Inspect the wires and wire connectors for dirty connections, damaged wire connectors, or damaged wires. Check on anything that may have gotten pinched, pulled, or otherwise abused while you where installing the head. Inspect the wire harness for any wires that may have moved or were not properly secured and may have come in contact with sharp sheet metal or hot exhaust parts. Inspect any and all wire splices for failure caused by the repairs. Inspect and test the fuel injectors and wire harness for damage or failure.