I have all the EWDs for every model year except 1993. I would think the wire colors are the same as the 1994, but I don't have a 1993 lying around to verify that.
The PO probably had a bad case of PHH puke in the connectors, and rather than clean them out, he butt spliced them. Or a "professional" stereo installer did it for him.
I will say that, since I'm refurbishing my 07-1995 engine harness, I have found that the pinouts and wire colors, for the EC1 connector (that's the pair you don't have), do not match the 1995 EWD. I was expecting that for my 01-1995, since it was sort of a transition year model and shares a lot of (undocumented) 1994 parts, but the discrepancy with the 07-1995 bothers me.
The EWD will get you from the ECU to the transmission. You'd have to take the harness apart to find which wires (colors, I mean) go to which terminals in the ECU and the transmission; there are wire color changes and splices in there that are not documented in the EWD. Not something I'd recommend for the faint of heart.
The EC1 connectors (those are the ones the PO cut out) are 90980-11087 (female, 12P, waterproof) (this is the engine side) & 90980-11086 (male, 12P, waterproof), and the terminals are type 2.3 II; you'll need 11 pairs. I'd go to
Ballenger (they're really helpful) for these; you can get them from Toyota, but their just reselling Sumitomo's stuff, and they're not assembling it for you, so why bother? The wiring harness manufacturer Toyota used wrapped the housings in foam; they don't come that way.
These are on pages F-10 (terminals), D-20 (f), D-197 (m) E-32, (both) and G-7 (both) of the wiring harness repair manual. There's a copy in the Resources section.
FWIW, I'd highly recommend getting a length of split loom for the exposed wires, or you'll really have a mess on your hands. You need some that is explicitly sold for engine bay and exterior use. In a pinch,
this will work, but not long term. This
PVC tape is a good match for the OEM taped ends of the split loom wrap; I'm using it to replace the tape I remove. Taping the ends of the split loom is at least as important as putting it on, IMHO. It doesn't create a hermetic seal, but it's pretty good at keeping most crap out.
HTH