Welcome to my world .... We have a 2013 JKU Rubicon and are going thru the same issues. Upgraded to 35's and with the stock 4.10 it was drivable but struggled on hills, dropping in and out of overdrive. Transmission started to hang in 3rd gear and bang off the rev limiter when pulling a hill. around town shifting was not a good as stock, but acceptable. Dropped the money to go to 4.88's and the results were less then desirable to say the least. Overall RPM at highway speed is very close to what it was with stock tires and 4.10 gears. Purchased the Superchips FlashPaq, corrected gears and tire size, Speedo now reads right on the money. (Think I ended up with 34.5 for the tire size correction). Transmission still did not shift well, really likes to hold on to a gear before upshifting under load. (Autostick will not let me manually shift up either.) Under full acceleration on the flat it will not shift past 3rd unless I let off the gas for a moment. On hills I am screwed and stuck at 55-60 with engine screaming, steeper hills it will hit second.
I did a lot of research and many others having same issues. I did find two companies RPM Extreme and OST Dyno that sell reprogrammed TCM's. Reviews of both were pretty much hit and miss, I contacted both with what my symptoms were and if it would play nice with Superchips etc. no response from OST, and had some good conversations with RPM. Decided to go with RPM and ordered their TCM, installed it and noticed a big improvement over the around town shifting, nice and crisp at a reasonable RPM, however the wide open throttle and climbing hills were virtually unchanged. Started getting oil in my air filter which never happened before the change, but I had not taken the Jeep on a long mountainous trip since the bigger tires so I think the oil issue may be more to do with running hard at high rpm for an extended time. running around town does not seem to be creating the oil issue, so I am sure that is not the TCM fault. I am currently emailing with the rep from RPM and It looks like we are going to send the TCM back and he will adjust some parameters and send it back. Hopefully I will have some better results.... Not sure if I will try the OST Dyno TCM if I do not get results out of the one from RPM or not, gets expensive, but not happy with how it runs now, and willing to do what it takes to make it shift normal(ish).
Had thought about purchasing an HP Tuner and having a go at programming it myself, but after reading many hours of posts on wrangler and HP Tuner forums, no one else seems to be having any success. At least with my own tuner, I could keep tweaking one variable at a time until I find something that works. Other thoughts have been a 8 speed auto conversion, or a Hemi/8 speed swap...lol