1997 Dodge Neon anti theft alarm will not reset

Battery went dead. Tried to push start(5 spd.). Car would not start. Pushed car back up driveway and anti-theft alarm went off. I thought it might be because battery voltage was so low. Replaced battery and alarm started going off and the only way to shut it off, is to remove ground wire at battery. I tried cyclling the drivers door lock with the key with no results. I also tried unlocking the passenger door and trunk. This has been going on all week. I would like to know if the computer is seeing an open from the enabling switches. Or if wecan jump the ecm. To get the alarm to shut off and to get the car to start.

updated 11/25/08

Alarm would not reset by having key on and connecting battery etc. I dropped the lower dash sections and located a module with 4 wires (bl.R. Bu.

wh.). It has an adjuster for + to -. Looks like a pot adjuster. Also I can see where someone has cut and looped some wiring into the harness. My next step is to trace the add on wiring and see where it goes. The car is broke down by a friends house so I am running back and forth. I'll let you
know what I find. Thank you.