Car alarm help, car won't start Options

[lawngsx]

Well, I installed a TMO stage III two weekends ago. The car ran fine and by using the different options on the chip I was able to check and make sure it was an actual stage 3 (bought used). The problem came in when I went to run my clutch wire. Last year when a friend and I welded my clutch lever, he ended up disconnecting my clutch switch and tucking it up above the pedal assembly. This proved to be a problem once I wanted this harness again. So what I was forced to do was basically remove my entire dash. In order to do this, I had to disconnect some harnesses from the fuse box. Once I had run my new wire and put the dash back together I made absolutely sure I had the harnesses hooked back up to the fuse box properly. Once everything was back together I tried to start the car. I could hear a click in the engine bay and all of the electronics work such as the seat belts and lights, etc. but it still wouldn't turn over. So I did some troubleshooting and narrowed it down to the Viper alarm messing up. When I use the key fab to try to disarm the alarm I hear a click but nothing else happens (doors don't unlock). If I open the door and unlock them, the key fab can then lock the doors though. This tells me there is something that the alarm doesn't like that's telling it that the alarm has been tampered with. So I went under the dash again. There are 3 or 4 loose wires that are stripped, I tried every combination I could think of and still nothing happens. I also checked the fuse on teh alarm and it is fine.

What could I be missing?

If nothing else, I need to pull this alarm out. Does anyone have any idea how to do it? Is it simply going to be unpluging some harnesses adn then pluging the stock stuff back together or is this alarm goign to be spliced into my ignition?

Thanks a lot for the help guys. I was jsut going to try to go along and check through the whole mess but I'm goign to need this car running in 2 weeks so any help would be much appreciative.