What I was trying to say is you are adding complexity to the tune by not wiring it up like GM did. You are spending loads of time troubleshooting issues that simply wouldnt exist if you connected the CPP to the PCM. It is great that it is working without it hooked in, but I think you're running in circles trying to figure out a way around a simple issue that is easily remedied. To me, the easiest way to find a solution would be to run the wires to the PCM from the CPP and any other sensor that a factory manual truck would have so it is exactly like GM would have wired it. Then start with all of GM's stock settings for a 4.8L manual (only one I know that came with a manual) and start tweaking from there.
I do not know exactly how the PCM determines gear with a manual trans, I think Joe posted about it a week or two ago. I believe it is a combo of RPM and VSS, but dont quote me on that.