At this point without actually being able to check it out for myself, all I can tell you is that I am still confident that it is a wiring issue in your harness somewhere between the injectors and the ECU. I don't have access to an 89 specific wiring diagram so my advice may or may not help you as to where the yellow wire goes. I can tell you that an 88 and earlier models have a resistor on the fender that those two wires would go to. Since yours does not then I would assume that the yellow wire is a common ground for many different sensors and components. With that being said, each wiring harness has many different points where they are grounded to the vehicle. So, back to my original advice is to pull your engine wiring harness and cut it open. Mark which plugs are your 1 and 3 injectors. Cut the loom open and inspect or replace all wires going to those injectors.
FYI: If it's not worth it to you to repair that harness, you can ask around on yotatech and pirate4x4 and maybe you can find a harness specific to an 89 4runner. I replaced the harness on my 88 because the p/o rat FU^KED the whole thing. I paid about $150 for mine but I found mine that was in mint condition and un molested. Normally you can find them for between $50 and $100 shipped.