Just some quick thoughts, I have personally installed a new alarm system and a stereo head unit into my cd5, I can assure you the alarm system is nowhere linked to the stereo head unit.

When I installed the alarm system I notice the wires underneath has been cut for 1-2 times which indicate the previous owner (or maybe the one before that ) had disconnected the factory alarm system and installed an aftermarket one in it, so I guess now it's my turn......

So why don't you just disconnect the old alarm system and installed a new one in it if you know how, alarm systems are readily available in ebay and there are cheap as chips. I believe the entry level alarm system today will be way better than a premium alarm system 15 years ago let go the fact that our CD5's original alarm system may not even be a premium one....