well lets start with the basics, What head unit are you running?
Taking your HU out and hooking up outside the car is a good idea. Start taking pieces out one by one each time testing your gear. My guess is if your factory alarm is messing up you got an electrical issue with the car itself and not your gear since you took your amp out and it works in someone elses install.
I installed a Kenwood HU in a Honda CRV with the factory harness ect and the deck went into protect due to the security system being tied into the factory harness for the stock HU. We had to get another harness to loop the ground for the factory alarm and after that the deck fired right up and has been working great ever since.