Wont start

I have an unusual situation... Well when I bought my car 2 years ago, I was never given a keyless entry or alarm keychain. Yesterday I realized I locked my keys in the car, but i left the window down a couple of inches, so i grabbed a pole and unlocked the doors... the car alarm started to go off. i thought if i put the key in the ignition the alarm would turn off and the car would start.... neither happened.. After about 5 min of the alarm going off i had to disconnect the battery. I took out all of the anti theft fuses, and the alarm shut off... but now my car will not start.. when i turn the key I get all the lights, and the fuel pump primes, but its as if the clutch is not being pushed in all the way. I got on the floor of the car and pressed the clutch sensor in by hand and had my girlfriend turn the key... the car still would not turnover or even attempt to start. i replaced the started 6 months ago, the starter signal fuse is fine, and nothing seems to be out of the ordinary.. Its gotto be something with the alarm.. anyone that can help PLEASE