does the secondary alarm have a remote start function ?
is there a pellet resistor in the key ?
is it a factory key that you use ?
before you do anything else would you just take the drivrers side knick panel down and check to be sure the alarm system (aftermarket) ahs any blown fuses or plugs that have came loose ?
you need to access the ign lock cylinder to expose the i believe three small wires one of the when cut will simply appear as a sysem fault to the computer and lock the system out ...problem is i did this once on a different vehicle and cannot remember the color...i wanna say it was red white or gray , i am sorry but cannot find an exact schematic for this truck and actually would recommend you just take it to a alarm shop to fix the bypass module fault - good luck
this is the instruction i followed...also to note is that we don't really know how this might work with the way the other alarm system is hooked in - good luck