2000 navigator relay clicking and windows only work with dome light on when vehicle is shut off the dome lights flash for several seconds the wipers quit working also where do I start?

The place to start is to have diagnostics run , checked or what ever you would call it , every body on here calls it something different . The GEM - generic electronic control module controls subsystems like power windows , power door locks , interior lighting an other functions by energizing relays ! An can store DTC'S - diagnostic trouble codes , There may be a light lit on the dash like a wrench symbol or maybe not ! You would need a factory or a up scale scan tool , not a code reader because this only checks engine codes . When I see vehicles with problems your experiencing I tend to look at the module controlling these systems , if no codes I check power an ground circuits ! Lose connections , corrosion .
The generic electronic module (GEM) constantly monitors its subsystems for concerns. If a concern is found in one of the subsystems, the GEM will record the concern in the form of a diagnostic trouble code (DTC).
The ignition switch position is very important to the GEM function. Often times, erratic or unexpected GEM function can be traced to problems with these GEM inputs.
The GEM controls the following features:

• Wipers/washers (front/rear).
• Warning chimes.
• Battery saver.
• Illuminated entry and courtesy lamps.
• Driver power window.
• Accessory delay.
• 4-wheel drive.
• If your not up on automotive electronics an electrical testing I would suggest you take this to a ASE certified automotive repair facility ! You could be way over your head on this !

All these components are controlled by a computerized module. You can try disconnecting/reconnecting the battery as this may reset the module. If no results you will have to have this modules operation checked for any codes/failures with a scan tool to possibly pont you in the right direction