Think you are going to have to do a pin by pin trace of your harness. I can't remember any vehicle with a 16v that used 2 six pin connectors to make connections in the rain tray. Can't remember any vehicles that do for that matter. What vehicle did the engine come out of? Are those wires/connectors part of the engine harness or another harness or mixed? You say "I am told . . .", does this mean you purchased this project unfinished?