Mine doesn't have brake or clutch signals. Also don't remember anything in HP tuners about A/C being deleted but I could be wrong there. Have you had a look in HP tuners at what settings are enabled?
When you say there are no faults do you mean the MIL light is off, or a scan tool says no faults, or both?
The VSS on the gearbox outputs a high and low, so yes they could be backwards.
I have an LS3, but it's an E38 ECU.
Can you define "hairy dog" please
