Yeah Ford used a TCU (trans control unit) separate from the ECU (engine control unit) for the first several years of the E4OD. It was the first electronic automatic for them (C4, C6, AOD are all mechanical) and the transmission controller was a stand alone unit. GM did the same thing, as I have a 4L80E TCM from a 93 van I've held on to just because it's unique and the aftermarket pieces are pricy. I think Ford switched from separate ECU/TCU to combined PCM (powertrain control module) in 1994 maybe, think airbags was a contributing factor. Been too long since I knew but a 1993 5.8 ECU (no trans control or sensors) or a 1994 5.8 M/T PCM (engine and manual trans sensors) might be what you need. (Assuming I've remembered the years right, might be 94/95, etc)
The manual and auto trans connectors for the computer are typically the same plug for Fords, the wires are just in the wrong holes. Disassemble the plug, move wires, reassemble, done. Doesn't mean the computer works, just no hacked wiring harness.
Aftermarket tuners (plug in chips) can usually make an auto PCM work with a manual because it's just deleting stuff whereas an auto trans and manual computer would require adding stuff which is harder. I know this from experience with Ford diesel trans swaps (ZF5 for E4OD) but it may differ or not be common for the gassers.