Help With Stupid Alpine Alarm

[Jim C]

Dunno if anybody might be able to help, but I'll try anyway.

I swapped KAEs on my beater s13 a while ago.

The car had been strted multiple times while diagnosing random issues.
Today I went for gas, and after having the car filled I got into my car, turned the key, and the alarm went off.

After trying a few things (the remote's battery is dead), I disconnected the negative terminal and cut the power to the loudspeaker.

I found a friend close by to bring me a battery out of his for it.
The remote seems to be working, although it won't unlock anything.
Anyway, nothing worked, so basically I was looking for feedback as to why this might be occuring.
Is it possible that something could have shorted??
Maybe something was changed during the engine swap?

Any ideas?

Thanks