You can repin the auto harness to work with the manual ECU, but it is a pain. And depending on waht year the auto harness (97 it seems) the plugs copuld possibly be different than the manual ECU that you purchase. Early year Auto ECU's used the same plugs so I think you will be ok.
For way more info on 3.4 swaps, including a ton or wiring help go here--->
www.yotatech.com/f160
