Charging system problem

Hi, I have a 1990 Oldsmobile Toronado Trofeo. I got it and it had a busted rod because it had been run with a problem. The 3rd cylinder injectror always squirted gas, thinning the oil. I replaced the engine and have everything back on, but it still squirts gas in that cylinder. I decided it was an electrical problem. It showed codes 41 and 47 one 41 being camshaft knock sensor and 47 being the ecm not communicating with the bcm. I replaced the ecm and this did not solve the problem. The alternator does not charge the battery, I believe this is the problem. The battery remains at 12.5 volts with the motor running and off. When the alternator/s was tested on the car it failed, but off it passed, is There an external voltage regulator I need to replace, or is this a wiring problem. I should also state that with the car running is misses and the egine ran fine for the first five minutes I had it in (the battery was fully and freshly charged). Inside the gauges do not work unless you flip the lights on then when u do that the radio backlight goes out, but the radio still works. I believe this is the positive cable on the alternator, how do you fix this the wire goes all the way back into the firewall and is nearly impossible to find, and how do you test the wire. Thankyou any help at all would be much appriciated