After speaking with Power by the Hour, the lack of wiring harness for the Gen 2 or 3 (in an 05-09) was the reason I chose to go with a built 3V rather than a Coyote swap. My power goals were more than a Gen 1 could take . . . unless I was willing to build the Gen 1. By that point, the cost didn't make sense to swap.
They did say a Gen 1 wiring harness could be made to work on a Gen 2 motor, but there were be some issues, particularly on cold start.
If they had a plug-and-play harness for the Gen 2/3, my build likely would have gone a completely different way. I'm excited to see how yours turns out.