I had to put in a new alternator in my 99 Isuzu Amigo. The old one burnt up. Everything seemed fine...output was around 14.4 volts, however, the plug that goes to the "S" & "L" terminals on the alternator had partially melted so I ordered a new one. Well, I put on the new plug by twisting the wires real good and covered them with heat shrink tubing. After doing that my battery light came on, my alarm no longer works and my OBD-II connector no longer works. The output voltage was reading around 15.6 volts. Then I read that the connections had to be soldered (not just twisted). So...I soldered the connections. Now, my battery light is no longer on but I still have no alarm or OBD-II connection and the voltage output is only 10.8 to 11.1 volts. Also, the battery is good and I can't find any blown fuses. HELLLLLLP!!
15.6 V will probably not do it, but ECUs and parts of them have failed from over voltage.
I believe that on your alternator there is a voltage regulator which can be separately replaced. Probably $15 to $20.
My suggestions are as follows:
Pull the alternator, and take it to the parts store. Most of them have a tester to bench test an alternator.
Once you establish that the alternator is OK, reinstall it.
You should not have to run the engine to get the ODB-II port to work. Simply having the ignition ON should give you access to the ODB-II interface. If it doesn't work just on battery, you will have to hunt that down.
You say your old alternator burned up. Do you know why? Is there some electrical issue in the car which is drawing a high current, so that the alternator ran at full output for an extended period of time?
Are other electronics in the car, such as the radio, still working properly?
It is possible that your ECU has been damaged, but that cannot be determined just by the information you provided.
You will also need to find the root cause of the melting wires, the blown alternator (if not simply old age), and any other car electrical problems.
If you have access to a DC clamp on ampmeter, it would be nice to know the current coming out of the alternator while the voltage is sitting at 11 v or so.