I'm sure people with more experience will chime in, but I was having 3-4 flare on my transmission (2006). Here's my findings..
ATF fluid...old ATF can cause this (what state is your ATF in?)
I changed mine...still same problem
4th gear isn’t getting enough hydraulic pressure fast enough which could be a lazy pressure control solenoid, valve body issue, or worn seals in the clutch drum.
I replaced my TCC solenoid and valve body...still same problem
The PCM *can* cause this, but unlikely. In fact Wrangler Fix says their PCM can help cure this, not cause it.
I replaced PCM...still same issue
rebuild kit for your transmission will be the next step.
In my case, I had a major seal breakdown and ATF sprayed all over the underside of the jeep (over heated ATF probably), so I have decided to replace the transmission with a remanufactured assembly (I suffered teh occasional judder in other gears too, not just the flaring from 3-4), and install a trans cooler. I'll let you know what the outcome is in a couple of days when its done
I should note that I'm also re-routing the trans cooler lines since they pass near the cats which isn't going to help cool anything down!!