aladdin on mustang

For some reason the car will not remote start.  Its a 98 Mustang, It is a manual.  I have not cut the transmission wire, and I am using a transponder which is hooked up to the a-2000.  I connected the clutch wire to the start assist wire, the brake wire is working, ignition and starter wires are hooked up.  But when I hit the remote start button the alarm siren just beeps twice and does nothing.  It does not even make an attempt to start it.  I do the sequence where you hold the brake and pull the key out.  Get out of the car and let it shut off by itself.  Then I hit the start button, the two beeps, and nothing.  Any ideas?

Ya, I pulled the ebrake, left it in neutral, pulled the key out(car still runs), got out of car.  Let car shut off and arm by itself.  Then i pushed the remote start button, I get 2 beeps from the siren and nothing.  I saw it in another post but cant find it now.  How do I wire the clutch so it is bypassed.  So i can start the car without the clutch being pushed in.  Because in that case I can wire the remote start as if it were an automatic.(which is how it was in my old car, and I never had a problem).  Other than doing that I cant figure out what the deal is on why this isnt working.  Thanks!