The factory alarm is on the floor under the driver's seat. Sometimes they put it under the carpet. I bet what's happening is a bad ground or door pin switch making the alarm go off.
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'88 Pathfinder: 6" of lift, 33x13.50 Swamper LTB's, Rancho 9000's, L&P Stage 3 steering system, K&N, Pacesetter headers and 2.5" exhaust, Lock-Right locker, 110A alty and electric fan swap, dual batteries, 700W+ worth of PIAAs, etc.