on the 4l80 swap with two vss sensors you have to add a second vss sensor and pin it at the pcm for it to work correctly. So if the trans has a second vss you might consider doing some reading on the 80 swap and give that a shot. pm me if you want a place to get that rear vss harness.

 

I hear you, when we first turned it on, non of the driver side cylinders were firing ended up being 4 clogged injectors

 

But this is not an 80. The second sensor in these late model units is whats called a turbine speed sensor. Basically monitoring the input shaft. In this case and with the computer that is being used it is really not an issue. I do agree with what has been said here that the issue is with the VSS not working. I myself would look at the connector to make sure the wires are good. If all looks well I would back probe it with a meter.

 

How do you back probe

 

Use a paper clip to insert into the back of the connector. Then use your meter to check for the pulses the vss sensor creates. Off the top of my head I can not remember what scale to use. Its been a while since I have had to do this.