Rep Power: 0

I have a 04 civic ex. One day I had to replace the alternator but forgot to tighten the bolt that connects to alternator from wire harness. In result of that I fried the ECU. Battery light came on. Car went into limp mode. And reader wouldn't connect to my car.
Checked fuses and they were fine. Didn't change anything else. Got another ECU and had it programed to my car. When I went to pick the car up the battery light was still on but car drove fine for like 5 miles. Till it went back into limp mode once again.
Checked all fuses and they were all fine. Decided to get a different wire harness to put in, changed ecu and ignition ( so I didnt have to pay 100 to get another ECU reprogramed), changed battery fuse. Then decided to try again.
Started the car and no battery light and it ran perfect. I test drove it and it ran fine for about 40 mins. Went to work and left. On the way home I was at a red light, I took off like I normally do and around 3k rpms my car went into limp mode again. And scanner couldn't connect to my car again...
Any idea what else would be causing this.?
Im planning to get another EM2 shell, but I plan to buy a new alternator this time but don't wanna fry another computer.

 
Rep Power: 223

Did you ever tighten the loose bolts?
Check that they're actually tightening and they're not stripped.
The alternator grounds through the case so make sure the mounting surfaces are clean and shiny and making good contact

 
Rep Power: 0

From what I can tell it's not stripped. They seem pretty tight. Before any of this happened the long bolt that goes through the alternator was lose but it didn't fry the ecu when that happened.