That grey box (pax side, behind the lower panel, under the glove box?) is the TCU. I believe that the auto harnesses were largely similar to the manual harnesses - note that you also will have two connectors for the TPS (the auto used a "two-in-one" sensor, with half for the transmission) and the second connector - the four-pole one - will go unused.
You may or may not have trouble otherwise - I think the "C101" connector was deleted sometime in 1988 or 1989 (the bulkhead connector,) and you may have to work around that.
I wouldn't bother to leave the TCU plugged in - there seems to have been some difference between the auto and manual ECU, and if that is true, the ECU may look for inputs from the TCU that it won't get (if it's not there, it will probably think you have a manual - which is true. I can't verify this at the moment, however - I'm workin' on it!)
If you can post a pic of that connector you're asking about, that would help. The only ring lug that should be on the back of the RENIX alternator from the factory should be the 6m/m ring for the battery output post - the regulator connector is a non-standard Delphi Weatherpack. The other end will seem strange (at the starter motor relay) due to the segment of 10AWG fusible link wire - the rest of the lead is a 6AWG wire.