LLY Ecm detect protocol failed

I tried to read a LLY ecm in the truck with my HPTuners and it was getting a bootloader failure. I removed the fuses mentioned in the sticky but no luck, so I built a bench harness following some instructions off an efilive page and I still cannot connect to the ecm. When I connect my hand held scan tool i get an error and it will not connect either. I can connect to a ecm through my ls bench harness just fine. I am not sure if I am dealing with a junk ecm or if my MPVI2 will read over the class 2 serial or needs can connection?
Any advice?

My LLY bench harness is setup like this:

OBD2/ connector --------Blue ECM connector

Pin 2 --------------------Pin 16=serial data
Pin 4+5 ------------------Pin 8=ground
Pin 16 -------------------Pin 5+ Pin 10=battery