Background:
I purchased the Jeep stock in 2017 and had the steering/steering related suspension systems redone due to wobbles as part of the work done when I lifted and replaced the tires. This was around 105k miles.

Issue:
I am now at 170k miles and having transmission related issues that occur usually on the highway, but sometimes can happen during rapid accel or decelerations. The issues are usually hard or long shifts but I have also notices a shutter that occurs at certain speeds. The shutter sometimes feels as though its one side of the vehicle and sometimes happens during turns but I believe that may just be coincidence as it happens other times as well. I have had quite high revs on the highway at times especially when trying to gain speed up a hill. It happens momentarily during what seems to be a down shift. I want to note that I do run 35" tires and the jeep has been programmed for this but the axles are still geared for stock tires.

Things I have tried/More background:
While on the way to work today, I turned overdrive off and shifts were subtle by comparison. The issue only seems to occur when OD is on.
Transmission fluid has been checked and is red with some slight browning but not much dipstick had some residue, but it was not plentiful in the fluid.
Transmission only has the stock cooler, this transmission is known to get hot especially when off-road, I have had this happen but quickly stopped and allowed it to cool.
I also know that Chrysler has reflashed ECU to fix shift points but don't know if this vehicle has been reflashed/etc
I also know that this issue has been caused in the past by corroded wiring harnesses and just want to rule that out as a potential cause as well


Additional information:
I have already purchased a new 42RLE transmission I intend on swapping, however I also have one and potentially two cracked manifolds. I have not yet taken the heat shield off of the passenger side, but have filled the crack on the drivers side temporarily pending a part that is on the way to fix this permanently. After filling I immediately noticed a power increase.

Question:
I have gone ahead and purchased the new transmission as I found a deal on one that I couldn't let pass, however I want to be sure that there isn't any underlying additional problems that could cause this such as vacuum, exhaust manifolds, electrical, etc.
I am a college engineering student with moderate access to tools, but no shop to work in and will have to do the transmission swap myself at home. Is there any specific things I should look at before that undertaking? Additionally, while there are there any additional things I should look at replacing such as the rear main seal, adding/replacing a cooler, etc? Should I go to the dealer and have them check for an update first?

 

A couple of issues I see are: Only the stock cooler installed, and larger than stock tires installed without being regeared. The 42RLE doesn't like either of those.

The high rpm downshifts you see, (O/D on), are likely the result of the computer waiting too long to unlock the torque converter and downshift to 3rd. This usually causes it to have go down to 2nd to make up the speed.
I have stock tires with 4.10 gears. Driving 55 mph and less, my O/D is off. I hit the button as soon as the engine is started.
On the highway, at the higher speeds, O/D is on, but I hit the off button at the beginning of an up-hill stretch. This unlocks the torque converter, shifts from O/D to 3rd, and re-locks the torque converter. If, on the hill, it needs more power, it unlocks the torque converter, and stays in 3rd. That avoids those high rpm downshifts.
An unlocked torque converter generates a lot of heat. That's where the additional cooler does its thing.