1998 1.6el engine swap alarm problems

[wsc_el]

I just had a JDM D15B OBD2 VTEC ENGINE put in my el. The 1.6 seized and this was the cheapest fix. I got my car back from the garage and the alarm goes off at random times. Sometimes 5 minutes after I arm the alarm and sometimes hours after, like at 1:00am. This is the factory alarm and I have had to pull the horn fuse to stop the noise, however, this doesn't stop the alarm from going off and I have to put it back in when I go somewhere because it is also the fuse for the brake lights.

Is there something that could have been missed in the swap that is causing the alarm to continuously go off or is it probably just something unrelated.
If there are any possible solutions I would like to investigate them first.
If not, how do I disable the factory alarm and does anyone have a downloadable repair manual for this car that can help?

Thanks