Running codes may not work without the round plug under the car hooked up. ( if its the neutral switch )....or if the clutch switch isn't hooked up. That is a built in safety feature so you can't run a KOER test with the car in gear. That would end real bad.
One of the first things is identifying everything that isn't plugged in. Then you need to dissect the added wiring to see where the PO tapped in to stuff.
The car runs and drives....that's way more than half the battle. You know it has the stock 86 computer so the wiring should be the same as an 86 5.0
There was a way that people would wire a MAF sensor into a speed density computer like yours. I don't remember off hand ( that was at least 15yrs ago ). I don't think an 87+ computer would work on your car because the dash harness is a little different.
You need a good wiring schematic for your year and model car. Then you need to trace and repair all the botched up wiring.
The emissions stuff usually won't cause driveability problems....other than pinging from no egr function on hills while cruising ( light throttle ).
The ECT sensor is very important. If the car doesn't know how warm it is it could cause a high idle condition, rough idling, and stumbles while driving. There should be two on your car. One temperature sender for the stock gauge ( one wire ) and another for the cars computer ( 2 wires ). There should also be an IAT sensor....it goes in the intake and read air temperature.
The air temp sensor and coolant temp sensor look almost identical other than the very tip.