Driverside Door replacement need alarm reset?

I just purchased a used 99 Ltd 4Runner and it had been in an accident and the driver side door and driver side back door had both been replaced after the accident (some time ago). The problem is now when I try to unlock the drivers door either using the key or the remote, the alarm doesnt disarm. Toyota says that the alarm doesnt recognize the "chip" in the replacement door so it doesnt know its unlocked. They say they will have to tear apart the door to figure it out. I think that will be expensive! Also, the auto all door lock, after I start the car, doesnt work. I am sure this is all related. The remote works to unlock the drivers door when I hit it once, but the alarm wont disengage.

Does anyone have any ideas on how to fix this? I downloaded the specs on how to install Toyota's alarm, and it looks like there are two connectors for the drivers door, but dont want to monkey with that if someone else has a fix for this.

Thanks!