MY 94GT had keyless when I got it, but no key fobs. The guy I bought the car from didn't even know it had it! But when we brought it home, we looked around in the truck, and there was the box.
All we had to do was find 2 key fobs from another 94-95 Mustang. Open your driver's side door. Then you put your key in the ignition, and flip the switch forward about 10 times. Flip it all the way forward to where you would be starting the car...you know, to the point that the dash lights are coming on.Then leave your key in the ignition, in the off position. After doing the switch flip 10 consecutive times, your door locks should respond by going up and down a couple times. At that point, start hitting buttons on your key fob (that you should be holding). The key fob should pick up the antenna signal from the box in the trunk, and should start working. Just be sure to get keyless fobs that are from a 94-95. If you get any newer than that, you will have to change the box that's in the trunk.
I can't say whether the aftermarket alarm will play a role in whether your key fobs work or not, sorry. It may or may not affect it, depending on the alarm, how it was wired, etc...