That 4 plug harness looks like the one that should be on the front side of the engine between the fuel rail/front valve cover. The second plug looks like the coolant temp sensor plug. Are you sure you have your wiring harness laid out correctly?
As far as the shift interlock issue, I had the exact same issue when I switched my engine (among other issues too) and it turned out to be the two small ground wires coming from the starter harness. Make sure those two wires are bolted up to the bell housing stud where the large ground strap connects to - should be a 18mm nut on the stud, then a 15mm nut to hold the wires in place. Also, make sure the wires and the stud/bell housing are clean and shiny - when hooking up electrical wires remember this: clean and bright, nice and tight.
Hope that helps!
