Well, my friend, you are living everyones worst nightmare for pulling wires and aftermarket electronics. Gotta concentrate on the alarm wiring, maybe download (if available) installation information for the alarm system. Good luck trying to find diagrams, I've found them hard to come by.
I have an aftermarket alarm in my 996 that works, but I never use as my car is garaged and we live in a pretty safe area. I find the system annoying as the keyfob would go through batteries about once a month. Also, if we ever made the mistake of trying to unlock the armed car with the factory keyfob, all hell would break loose with an alarm that was hard to disarm (as battery in alarm keyfob was weak). I stopped using the system and thought of removing the electronics but was concerned of running into the exact issue you've run into.
As I've been unable to locate the schematics, I've decided to punt for now. My factory keyfob works great and so it goes!
Your problem may be difficult to find but it will be easy to solve! Hang in there!
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