Rep Power: 0

car:
03 civic ex coupe

changes to car leading up to problem:

-ignition lock seized between 0 and I positions

-disassembled it to try and fix on the spot

-had locksmith come and fix it and made new same cut key with previous key's chip

-car worked fine until I closed door with key (enabled alarm) and could not disable alarm until I disconnected immobilizer connector from ignition lock
*alarm/keyless entry worked with that connector unplugged but had to reconnect to start car*

-ended up just ripping out aftermarket alarm but keyless/stock alarm doesnt work still (didnt try without immobilizer disconnected this time) however the remotes do get programmed by doing the on-lock-off-on-lock-etc method

-however something I noticed is that when I open door (without key in ignition) I get the beeping noise (isn't that just for when key is in ignition?), could this be problem? how can I fix this?
Thanks for any information in advance.