Car Alarms: disabling alarm, jumper cables, toggle button

Question
I have a 2003 Honda Civic with a dealer installed alarm.  A few years ago the keyless system stopped working and I would manually lock the car with the key.  This was not a problem except when the battery died and I had to jump start it - although I was able to disable the alarm by using a small toggle button under the hood release.  A few days ago my battery died because I left my lights on and I went to jump start the car and as usual the horn went off but this time I couldn't disable it using the toggle so in frustration I pulled out the wire to the toggle button which also didn't work.  Lo and behold I realized that in my haste I had connected the jumper cables to the wrong terminals on the battery and that was what had caused the horn to go off. Today I replaced the battery fuse and when I jumped the car properly the alarm went off as usual so I located the alarm box under my steering wheel and pulled out the 3 fuses that were in it - now my car has power but it won't star.  Is this an alarm issue or is it possible I fried the starter when I incorrectly hooked up the cables.  thanks

Answer
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If anyone can guide you on this,
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Good luck.

ALARMTEK