Alarming alarm problem????????

Last week i finally had to change the very tired battery in my wifes '94 model 2.0 GT. fitted new battery, but now alarm system will not disarm. can get to a stage of turning the motor over by switching ignition to "on" before connecting battery, but imobiliser will not allow the car to start. as soon as i turn ignition off, alarm goes off and i have to disconnect battery and then reconnect it to silence the alarm. i know the problem is in the resetting of the alarm system, but the manual for the alarm doesnt tell you how.
the system is a factory fitted "Toyota 5000 theft deterant system".
any ideas other than destroying the car would be much appreciated by my wife, and may even save my sanity and my life!!!!!!!!!