Alarm Killed my car !!!! HELP

well first let me say that i have a Viper 791 w/ window mods, shock sensor, motion sensor, and immobilizer bypass.

on monday 3/5/07 i have decided to "demodify" my sequoia
On Tuesday 3/06/07 i took out amp/box/subs/headunit.

after i connected the battery back my viper won"t work. so i had to use the key to lock and unlock my car.

on wedsnesday 03/07/07 I took my car to get the viper fixed. after the viper gets fixed my car won't start.

I have spent 8 and a half hours diagnosing the problem. i have come up empty handed. i"ve checked everything - battery,spark plugs, injectors, starter, fuel pump

one wierd thing that i"ve noticed is that the red light keeping blinking in the middle of my gauge cluster.

I brought it to toyota and they said that the factory immobilizer is fine, and so are your keys.

now im stuck. I have ran out of ideas. can some one give any suggestions. or have any ideas. PLEASE HELP ME GET MY CAR BACK UP AND RUNNING ! Thank you.