I did the internal regulator conversion while ago, since then someone worked on my car, and today i noticed that the #1 and #2 terminals on the alternator were backwards! What damage could this have done and what would it have been doing while being hooked up wrong??? i quickly changed it, and everything seems the same. Still get 12-13 Volts.

What do these terminals do?

Hard to say, should get around 14.5v max from alternator if regulator is working correctly. May have to bring rpms up off idle to see that output from alt. If all you see is 12 to 13, max, that doesn't sound good. A fully charged battery will read in that range. If you can't get more than that I would take it off and have it tested.

That reading is with my electric fans on, fuel pump on, amp and radio on. Im thinking it would read higherwith all of those off

That reading is with my electric fans on, fuel pump on, amp and radio on. Im thinking it would read higherwith all of those off
Maybe it would. Off idle if your alt has enough amps it should read around 14.5v. If it's reading 12 to 13 at idle with all those things running it's probably ok BUT until you see it charging at 14.5v or take it to have it tested it's impossible to say.