Passenger's side window goes down whenever I open the door I have tried to reset the bump stop but no luck. Has anyone else experienced this problem?

 

Sounds like a short in the harness in the driver door that's bypassing the switch. Bending / flexing the harness when you open the door is causing the contact between wires.

 

Cause of trouble can be in the wiring harness or connector between body and door

 

When I replaced the window motor in my Navigator I went through a helluva dick dance trying to get it to behave properly. It kept going down or half-way up no matter how many times I followed the programming procedure. When I finally broke down and read the shop manual I discovered that there is a de-programming procedure that you must do first so you may want to coon around and see if there is a similar procedure for your car.

 

Try to reprogram it then reprogram it.