What you have isn't really a stand alone box. What you most likely have is a PCS XFC box that DESTROKED uses to act as a J1850/J1939 gateway to provide the GM TCM calibration info for the TCM to shift. The GM TCM calibration uses J1939 I believe at 256 K to transmit engine data like throttle input, torque, and other engine data that the TCM uses for shifting, and it also provides the J1850 data for tow/haul mode(without a BCM), and overdrive lockout. As to the TCM, my bet is it is the standard GM 5 to 6 speed conversion kit for an 03-05 truck since that is what the DESTROKED gateway is setup to work with. My bet is BEANS just did the trans build to the 05 trans, installed the 6 speed conversion valve body, then installed the DESTROKED wiring harness for there particuliar setup, and went through the setup of the XFC box to read throttle input from the CUMMINS ECM via it's J1939 output.

Unfortunately your shifting complaints are all to common with the DESTROKED setup as SEVERAL others have had problems with the XFC box not outputting the correct throttle data, or the TCM not always recognizing the outputs. MANY have done away with the DESTROKED kit, and gone back to using just the ALLISON TCM, wiring in an analog TPS signal directly to the TCM(the ALLISON TCM will default back to an analog TPS once it doesn't see any J1939 data), and then using a GM BCM to trigger tow/haul mode. Since you already have a VP44 CUMMINS engine, you would be WAY ahead of the game to just go to an ALLISON dealer with a stock ALLISON 1000/2000 5 speed TCM, and letting them set it up with an ALLISON calibration that will make the CUMMINS ECM work directly with the ALLISON TCM. You would lose 6th gear, but you would gain a FULLY functional engine/trans combo. The ALLISON TCM can easily be set up to read engine data directly from your CUMMINS ECM via it's J1939 databus, and get all the data it needs that way. And since you're working with a 5500 truck, any ALLISON dealer can work on it without violating the GM ALLISON sale agreement. Theres one other option, but I don't want to post it in open forum, and I can't send you a PM to tell you. But there is a shop who can probably get you working with your current setup IF you can get him to make the time to look at it.