92 Jeep XJ running rough (intermittently) with Codes 12 & 41 (did not disconnect or touch battery)

My Jeep had been sitting for about 4 years before I started driving it after my bf totalled my daily driver. It was my dad's and he took great care of it until an intermittent starting issue frustrated him enough to let it sit.

Since I've been driving it it's had the drive belt replaced, CPS replaced, ignition coil replaced, and some spark plugs.

CURRENT ISSUES:
So for a while it's been taking forever to crank. (Hopefully I'm describing this right). I'll have to try to start it a few times or hit the gas. It didn't used to do this. Additionally there are times where I'm driving that the car seems to resist acceleration causing a shake. Took it to the shop they assumed I was imagining things it has been getting worse. I finally took the car on a longer trip and after driving about 80 miles I got a check engine light that stayed on. I checked the code and got a 12 & 41. I'm familiar with the 12, and have gotten it before after messing with the battery, but this time I had not done anything under the hood except add coolant and power steering fluid. Also I had checked before I took the trip and there were no codes. While driving back there were times that the voltmeter showed the battery dipping under what I assume was 12 but I it didn't enter the red box. It did return back to 14. I drove to AutoZone and they tested the alternator (in the car) and found no issues. The car starts (long crank still) and the code has not gone away.

So I've been reading forums and I know based on the code I need to test the charging system and will be doing that today Could it possibly be the ECM though? I saw on one forum that mentioned and wondered if that could be related to my other issues.

Any help is appreciated!!