I'm not going to lie, I'm hard on my stuff. My Autoprom is many years old...I got an earlier Autoprom from Mark Mansur back in the day, and that one didn't work properly either (he gave it to me with that discolosure) but I want to say it will allow you to at least datalog. Some of the issues I have may be self inflicted. I can't attribute the issues to how the truck rides, but I've noticed that the chip connections seem to be flakey. Sometimes re-inserting is necessary to get the chip to read and/or burn properly. Not to mention, the cables all over the place lead to the unit getting inadvertently jerked around when something drags across them, etc. And having the ECM hanging by it's wiring to hook the Autoprom serial cable up isn't my favorite either.
If you are stuck with the hardware solution due to the PCM, not sure what your other options are. But if someone has a way to control the trans and still be software-based, I'd probably go that route. Moates is a great company, always supportive of customers and the community, I just know the hardware stuff isn't as good for me as software would be.
I have fun doing the tuning, certainly better than burning chips over and over again to try and get things right.