First off, I think it's awesome that HP Tuners has added support for the 4.0 Jeeps. There are a ton of them out there, and stroker kitted 4.0's are becoming pretty common these days.
So, I reflashed my 99 XJ last night and there a couple of issues that I found. Since reflashing, I get a CEL (MIL) for P0700, TCM request for MIL Light. When I scan the TCM, there are no codes present and the trans shifts perfectly, converter lockup and all. Next is, even after I disable the rear O2 sensor in HPT Editor, A CEL will continue to pop up for low voltage on the post-cat O2 sensor. Neither of these are big issues since I can still make fuel and spark changes and the vehicle still runs and drives fine. Just the annoying CEL light.
Right now, I have it forced into continuous open loop and have been playing with my CO meter to make changes to the fuel delivery. I know it's old-school and not precise, but I'm waiting for a wide band so I can do some data logging.
That brings me up to the next issue with the scanner...
The beta scanner is still a little buggy and will stop functioning if you start opening up too many applications on your computer while logging (using a Dell M6600 with Windows 10 Pro, 32G RAM, and Nvidia Quadro K4000M graphics card). The scanner seems to confirm the issues with the mystery codes. The HPT scanner indicates that the MIL light is "ON", but doesn't display any codes and if you try the "clear codes" button nothing happens. Now... After the reflash, I did get a code for CAN Bus failure and I was able to clear the code with the HPT scanner. The other 'phantom codes' I can only clear out with my Matco scan tool. But the TCM and rear O2 sensor codes pop up again after a few minutes of driving.
Other that these issues, I'm pretty happy. Nice job HP Tuners!