I think that the problem is electrical. When all of the doors are shut, the interior lights will still come on. The gearshift locks so that I cannot switch gears. The engine will sometimes not start, although the battery is not dead and everything else turns on. Last night, the car alarm kept sounding randomly. I had to unlock the doors for it to stop. I took it to the Honda dealership, and they told me that I needed a new gearshift cable.
It appears that you are having multiple and intermittent issues with your Honda Pilot. Following the dealer's recommendations of replacing the gear shifter cable will likely only solve one of your concerns.
The issues you describe with your alarm may be due to the dome lights coming on after the car has been of and locked. This may be due to a faulty door switch that is giving power to the dome light and in turn triggering the alarm.
To be 100% certain however, I recommend enlisting the assistance of a certified mechanic, such as one from YourMechanic, to come by and inspect your Honda Pilot. They will have the experience needed to identify the multiple electrical issues your Honda Pilot is experiencing as well as make the repairs needed to restore the proper function of your vehicle’s components.
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