If installed properly the port installed security system should not have the ability to stop an already running truck. It is a starter kill system only and would only prevent the motor from being started from a non running state. I suspect they did something else to your truck other than remove the alarm.
It is really easy to disable. The port installers use a plug and play harness (at least they did on mine) You just remove the lower dash and disconnect the plug from the IGN switch. Remove the alarm jumper and plug the factory harness back into the IGN switch. It's that easy. You don't need to completely remove it since this operation removes it's main power source.
It killed it indirectly so to speak.
What apparently happened first is that the ciruit to one fuel injector
shorted; this was interpreted by the TVSS as someone trying to
hot-wire the ignition, so it shut it down,
or so I was told by the mechanics who troubleshot it.
I do know this; it died; just as if someone had turned the key
in the ignition, and, immediately, the horn started honking,
all at the same instant.
After I pulled over, I tried multiple times to restart it,
but as soon as I turned the key in the ignition, the horn would
honk, and the engine would not turn over.
I flipped the toggle switch on the kick-panel to see if maybe
it was in the wrong position, opened and closed all doors and
hatches and the hood to be sure they were all closed.
Nada;
The mechanics went into my harness and pulled out the one
bad wire, repaired it, and put my harness back together.
Saved me around $2000 by not telling me it needed a new harness
as many dealers would have done.
They did not have the repair manual, and it was the week between
Christmas and New Years, and they were covered up;
so they said they pulled out the TVSS and ran a wire to my ignition
to get me on the road. ie: that it might be able to fix it, but they
did not have the time or the manual to do it then.
I never messed with it after that experience.
Problem is finding someone who knows these systems and is
willing to fix it without charging you big bucks; seems like
everyone nowadays wants to make a days salary with one hour worth of labor. My rant for the day.
G