Engine and transmission problem codes P0700 and P0740

A few months ago I started having transmission problems, I took it to a transmission shop in the area with a lot of good reviews online and had it rebuilt. They messed up the rebuild and it was slipping so I took it back as soon as I could (I was away at college a lot this past year). The engine has also had a strange sort of murmur for awhile, but it was not really effecting the driving and it only happened at idle so I never thought much of it; it is an old Cherokee. I got back home for summer break and my dad told me that, after the car heats up, he noticed the murmur would happen and now the car kind of cuts out when accelerating. I noticed that it also sort of cuts in and out of acceleration while driving between 55 and 65 mph. The only codes that come up with the check engine light are P0700 and P0740. Having had transmission issues, I was familiar with these codes so I took it back to the transmission shop where they told me that the engine was misfiring which would cause the torque converter to cease to lock up which was why I was getting those two codes and that I would need to fix the engine and not the transmission. The problem is, there are no codes indicating misfires, bad fuel injectors, bad o2 sensors, etc, so I am having a lot of trouble diagnosing the problem. The coolant is new and full, and I replaced the idle air control valve, but that did nothing. Any thoughts?