Plug a known good ECU into your harness and see if the problems repeat. There isn't an easy way to test an ECU without a test bench and a good grasp of what you need for for signals. The 5V test is stupid, there are tons of things that can happen that won't show themselves with that test.. One of your signal inputs can be bad and the ECU still puts out 5v, I don't know who told you to do that..