Just thought I would update this thread.
So, I started having issues again within a few weeks, and worked out that $$% with the wiring under the dash would let me start it. It would be ok for a while, and then I would have to play with the wiring again.
In the end I took the car in and got the alarm replaced. The shop returned the wiring to factory before installing the new alarm. Haven't had a problem since, and it's been what, at least 6 months since the new alarm was installed.
p.s. mongoose (the new alarm) is the most annoying alarm I have ever had