Chassis swap, alarm won't turn off

Just got the car back from the garage after a chassis swap, the alarm enabled and locked the doors then started freaking out for a few minutes before finally disabling. It won't disabled or unlock the doors now though. Is it a case of the battery back up being drained and it's not happy or has something been forgotten to be hooked up? It's an after market cobra alarm cat1.

Fuses in the alarm blew, think it was cause the hazard switch and interior light switch have disintegrated and I am pretty sure each of them have an effect on the alarm, specially the hazard switch since it is wired into the alarm system. Ordered some new ones then will replace fuses and hopefully it will be ok.

Can manage to hot wire it with a wire from the positive battery to my ignition relay but the indicator fuse blows if I try and use them, guessing that is because the hazard switch fell to pieces.