2000 Mitsubishi Montero Alternator replacement

I replaced a failed alternator on our Montero Sport. When I reconneted the fully charged battery and went to start the car the alarm went off when the key was in the full accessory position. The truck started but every trouble light on the dash went on -- SRS, Check Engine, Alt, etc. Additionally when putting the car in drive the transmission shifted hard and a circle of green light around the N (neutral) indicator on the dash started blinking. The alarm stopped after a few minutes and I shut off the engine. I have checked all connections, they seem correct, the battery is fully charged, alt fuse is OK and the radio code has been reset. The power door locks do not work and the key fob switch does not unlock the doors either. I suspect that the inability to disarm the alarm either with a key in the door or the key fob and the fact that the power door locks do not function (power windows are OK) has something do do with the alarm being on / confused. According to the manual, if the alarm is set the engine should not start but it does. I have the alarm code serial number on the radio code card -- do I need to have the alarm reset? Thanks