Hard shifts can be caused by high transmission fluid pressure, which is controlled by the computer. Sometimes the comp will request high pressure when cold to prevent slipping. Next time let vehicle warm up a few minutes before driving. If it goes away, I would not worry about it.
I would not pay for a repair I did not authorize. If I was going to pay, I would have to see the old cables. If they discarded them, i would not pay. Do not trust them.
I used to own an repair shop and would always keep old parts for show and tell, and would love it when a customer asked...
Dating myself here, but I remember when I had my 1988 Ford Mustang GT manual transmission fluid changed by a local lube place, and freaked out when the guy asked for the ATF gun to add the fluid. I stopped them and they were sure it was the correct fluid to add. I left there and called Ford...
I would not worry about it,. A hour drive or so should charge them back to normal. If you want to charge them, I would disconnect them from the vehicle first. Probably not needed, but safer.
You can purchase the radio direct from Jeep (68297446AI) for $750. Why would you spend an grand here for one???????????????
https://www.moparwholesaleparts.com/oem-parts/mopar-multi-media-radio-68297446ai
The valve body is an electronic and hydraulic controller for the transmission.
https://en.wikipedia.org/wiki/ZF_8HP_transmission
PS the 8 speed transmissions are dirt cheap in the used part market.