This is another area Ive struggled with over the years with this swap, it *should* play nice, but no guarantees. That said, for the I6 the PCM controlled the engine and trans until 08 when GM switched to the E67/T42 combo. V8s only had a PCM for 03-04, starting in 05 they used an ECM/T42 combo.
That said, where did you get your 06 engine harness from? The only ones I can find on eBay are stupid expensive.