No problem, will be glad to help however I can. Soon enough I will need to get my harness laid back out again and finish some minor details. That would be the best time to ask questions, lol.
I know you can use the E69 ECM, but the E39 ECM can be used as a stand-alone but tuning knowledge may be limited. Not sure what other ECMs are compatible or what tuning capabilities there are for them. With the E69, you cannot disable VATS with HP Tuners so you will need to utilize the BCM and theft deterrent module, preferably from the same vehicle.
As I think I mentioned before, you can buy an ECM, BCM and theft module out of the same vehicle from LKQ and have it shipped to your house for somewhere around $300. I never thought about asking them to ship an entire TC wiring harness because the labor is pretty intensive to remove it. I do know they had several Cobalt TC’s in their inventory the last time I looked. Hell, you may also be able to get an SS subframe and control arms, steering column, fuse box and rest of the donor parts from them out of the same TC car too but the shipping could get costly. On the same token it would negate your need to even find a donor altogether.
A stock body wiring harness from an LS could probably just as easily be modified for a TC. The pull your own yards in Phoenix have several LS models.
There is only ONE company I know of who sells the E69 ECM to body harness connector, and they are EFI Connection. It retails for about $70. The rest of the connectors and pins I needed I bought through Mouser electronics. Most of the part numbers for the connectors can be found in the Chilton manual using the connector diagrams.