Mods delete please
 

Yes

Here is a schematic for 5V references. If you need any assistance please don't hesitate to ask. Just make sure you have the majority of them unplugged and find a circuit to test. If your test circuit is at 5V start plugging the other circuits back in one at a time. When you plug one in and your voltage drops on your test circuit you've found your problem. Check for shorts and opens on that circuit and test the component if possible.

Being as the clutch pedal position sensor does have a learn procedure and you have changed the relation of clutch pedal to clutch travel it may not be a bad idea to do a clutch pedal position learn. Unfortunately I don't know how to do it without the GM scantool.

Also a good point, I would expect a P080A set if this were the root cause but still a good idea once OP gets his issues fixed. I do not believe there is a way to do it without scan tool though. I would think a third party i.e. snap on would have the learn function but I could be wrong.

I re-read the OP, I would suggest looking under the clutch pedal assembly for a pinched wire. It's likely you pinched the 5v reference and it didn't make it through the insulation until you pressed the pedal a few times.

Thanks for the answers, I will try to get a look at wires and test them if I cant find anything that looks like I pinched it. Camaro2Tymer I made need some help on how to test the wires and 5v refrences.

Happy to help man, if you've got a simple multimeter that will work fine. You'll need some sort of small pin to probe the smaller terminals with, the ends of the test leads will be too big for some of them. A t-pin will work fine if you don't have anything available. The schematic shows you which wire you're looking for by color. Essentially once you have the majority of them unplugged go ahead and pick one that's easy to get to and test, probe your 5V reference wire and check your voltage. If its at 5V (key on) go ahead and start plugging the others back in one at a time until your voltage changes. If its not at 5V, you'll need to unplug more of them before testing. Once you plug one in and the voltage changes you've found the circuit in question. From there I can help walk you through checking the circuit and checking the component it leads to.

Edit: You'll want to reference from the top of the schematic, you'll see where it says 5V1 and 5V2, that's your 5Volt side. Those are the wires you're looking for.

Bump, still need help guys. Took it to a reputable auto electric shop and he said ecm but im kind of doubtful on that diagnosis.

Anyone? Pleaseeeeeé

Ttt, any help guys? I checked for continuity for all 5v reference wires going to the sensors on the 5v reference 1 from the ecm pins. All checked out, could it be one of these sensors going out but not throwing any other codes besides the P0641??

You checked continuity, but did you check for a short to ground or power?

I am going to check for any shorts to ground today, I checked all the 5v reference wires for power and get 5v on all of them also. Hoping i find a short to ground, its sort of the last chance of finding the issue.

Well after a month of checking wires and swapping sensors out. I decided last Friday to just try and drive it. It's fixed!!! Car runs like a raped ape again! No idea how I fixed it, I'm guessing by checking all the pins for the ECM and sensors I must have knocked something into place?!?! Too many sensors on these cars.

Just kidding, issues back a week later, did not change anything just randomly popped up while driving again. This car is driving me insane, looking at trading it in soon. And not for a GM...