I Had The Same Problem On A 1998. I Was Told It Was The Moonroof Motor. The Starter On Mine Is Already New.
The 2003 Lincoln Navigator is 6 ft. 8.2 in. (80.2 in.)1 one-touch power windows wide.
The 2001 Lincoln Navigator is 6 ft. 7.9 in. (79.9 in.)1 one-touch power windows wide.
The 2002 Lincoln Navigator is 6 ft. 7.8 in. (79.8 in.)1 one-touch power windows wide.
The 2004 Lincoln Navigator is 6 ft. 8.2 in. (80.2 in.)1 one-touch power windows wide.
The 2005 Lincoln Navigator is 6 ft. 6.7 in. (78.7 in.)1 one-touch power windows wide.
The 2006 Lincoln Navigator is 6 ft. 6.7 in. (78.7 in.)1 one-touch power windows wide.
In a 1999 Lincoln Navigator : In the Power Distribution Box ( which is " live " ) located in the engine compartment ( on the drivers side of the engine compartment ) (Maxi Fuse # 110 is a 30 amp fuse for the moonroof , flip windows , and heated seats )
There is a switch that allows you to open and close the Lincoln Navigator rear side windows. The switch is located on the overhead console.
Press the left side of the rear window switch that is located in the upper console on your interior roof
The wiring diagram for a 1998 Ford Explorer XLT can be found in the service manual provided by the manufacturer. If the power windows, moon roof fuses, and power relays are good but the windows and moonroof do not work, then it is likely a wiring problem
This is a guess , but check fuse # 14 - 15 amp - for ACCESORY DELAY RELAY ( power windows , moonroof , Flip windows )
check the circuit braeker