Like I said in my message, I removed the Allison harness and then ran new wires for what I needed. According to my notes this is what's needed when starting with a stripped harness.
VSS low- Green/Black, to ECM C2, pin 58, circuit 822
VSS high- Purple/White, to ECM C2, pin 45, circuit 821
Back up lamp supply voltage- Light Green, to underhood fuse box C2, pin A11
Ignition 1 voltage- Pink, to underhood fuse box C2, pin F8
The first 2 run from the VSS sensor on the back of the transfer case/transmission into the truck side engine harness, the last 2 run from the back up lamp switch on the transmission into the truck side harness.
Add a clutch position switch wire (CPP) from ECM C1, Pin 32 to C100 pin B.
4wd LOW signal from C153, Pin A to ECM C1, Pin 57.
More than likely the reason why your cruise isn't working is because you have a zf6 operating system flashed in the ECM but it needs the CPP signal wire before it will set cruise.