So after chasing down and correcting a wiring error and a related missing standoff / clamp, the clutch alignment tool ordered over a week ago, with two day shipping, finally arrived. It says "Ford 03" on it, what a surprise. Additional progress has been made:
I'll be installing the engine in the coming days. I have identified 18 connections between the car and the engine and made a checklist. after I have verified it, I'll post it for future reference.