Reprogramming Fob with Alarm Active

Hey All,
I just bought a 04 Tacoma PreRunner 3.4L last week and am brand new here. The other day I came home from school and had to go grab something back out of my truck and the key fob wouldn't unlock it. The fob will still lock it, but the unlock doesn't work. I have already tried a few avenues of reprogramming the fob mostly the one listed here: http://www.programyourremote.com/classified/2004-toyota-tacoma-listing-6522.aspx#.UzURKWBJ_PN

I believe my main issue is that I have an alarm that has to be after market (little blue blinky light to the left of the steering column and down a bit). While I am trying to reprogram the fob the alarm is going off the entire time, thankfully I knew where the horn fuse is and just pulled that so I could work in peace. The alarm is also hooked up to the ignition in my vehicle as I can unlock the truck with the key, but can't start the car once I am inside and the unlock button on the door doesn't work either.

I am really kind of stuck here and would appreciate any guidance to solve my key fob as I am currently stranded haha.

Thanks All,
Colin B.