Car won't accelerate past 40mph?

I have a 2001 Honda Civic EX. Recently the alternator "got loose," (someone failed to replace one of the bolts), and it fried my pcm. The dealership was unable to locate the correct part (no longer available), so I ordered an Acura part that was supposed to be compatible. I was told there was a difference with the emission code, or something like that (sorry, am not really sure). I installed it myself a few weeks ago. It ran perfectly well, but the engine light came back on after clearing it out. It was a catalytic converter error.

This weekend my car started having the same old problem… Unable to accelerate past 40mph. I unplugged the pcm, plugged it back in, and it worked normally again. However, it has happened 3 more times. Each time I unplug/replug it in, and it works normally. Is there something triggering the error that I can turn off? A sensor that needs to be replaced?

If you have experience with this type of issue, and think there's a work-around to keep my car running, please let me know. The dealership can't get the correct part, and will not work with a part that is "similar." I'm getting desperate, as I need this care for another 6 months. I'm afraid that I will get stuck somewhere, and not have a car to get to work or class.

Check your exhaust system for leaks!
One good source for parts is e-bay motors by the way.
But I suspect an exhaust leak is causing the check engine light. This kicks you over to limp home mode.

What trouble codes are you getting? Some parts stores offer to check the codes for free if needed. It may be best to get the right used PCM from a salvage yard or online site like Ebay and have it flashed by a dealer for your anti-theft system correctly. An Acura PCM may not be exactly compatible and could cause issues. Or if you can get the trouble codes, do a websearch with your model and trouble codes to see what they show… Could be some other part is defective and causing the car to go into limp mode.

A common problem was with code P1298… Electrical Load Detector (ELD) which could fail… Bad solder joint… And cause a car to go into limp mode… Might be related to the alternator issue as well. You may still have ongoing issues from the alt problem… Double check for any fried wires/connectors.
http://www.superhonda.com/forum/f49/honda-civic-2001-need-help-324982/

Either replace the PCM with correct model or find out what trouble codes you are getting and diagnose from there. Reask question or add details.

But wouldn't that cause a continuous loss of power? Why does unplugging and plugging my pcm back in temporarily fix the problem? I would assume a wiring/electrical/sensor problem, rather than a problem with exhaust, or other mechanical problem. But of course, I'm not a mechanic and don't play one on TV.

Hopefully you have the old pcm still and you can get the number so you can order another off ebay, there's a million of them on there. That year of Honda did have a problem with a capacitor going bad and there are people that fix them, you may want to research that as well.