The engine/trans harness you have has that one square connector, only the alternator/starter has other wiring going to it. That square connector plugs into the under hood harness, which covers everything forward of the firewall. That's where Ford made many improvements and that harness would be easier to connect to the engine and dash. I'd see about getting that and replacing your 92 under hood harness with it. Meaning use your end component connectors, but run the 98 harness out to those. That will let you use the 98 wiring diagrams to diagnose everything forward of the firewall.
BTW, the 99-01 under hood harness changed, and you need a 98 or older PCM, so try to use a 98 under hood harness. The 99-01 will work also, but then you would be mixing a couple of things about the 99+ returnless fuel system. If the 98 harness is trouble to get, the 99-01 is fine.