Some things to know/test I found on several sites and on here:
The computer only switches grounds. So actuators (like injectors) have 12v on one wire and ground/resistance-reference on others. Sensors generally have 5v on one side and reference on other (like ACT sensor).
The only place to get 5v is from the computer outputs between 26 and 46. SO:
Test across Pin 26 and 46 with volt meter - Should show 4 - 6 volts with key on. If not, you don't have reference voltage and ECU is likely toast in some way.
Pins 20, 40, 60 are all ground all the time whether ECU is in or not.
Pin 46 is a filtered ground that is switched by computer, so will not show ground without computer, but should when it is installed and powered on.
Pin 37(and 57, they are tied together) should have 12 volts all the time when computer is in and key is on. This is also where all your injectors get their 12v to actuate from. So you can test all the red wires on all those too to verify harness. The other wire on injectors will switch to a ground only when ECU fires injector, thus the need for noid light.
Pin 22 is a ground that is switched by computer to close coil on fuel pump relay. It also goes to self test connector, so you can look for switched ground either place.
Rather than try to explain other stuff.. This link will help a lot.
http://www.veryuseful.com/mustang/tech/engine/images/88-91_5.0_EEC_Wiring_Diagram.gif
That is the stock pin out diagram for the ECU connector. You can test from ECU plug end and sensor ends to make sure your harness is good. I have been doing this a lot lately, and ended up with a bad ECU straight out of the reman box from Autozone.