Have a brand new and tested alternator, battery, cleaned all connections checked all the fusible links and still not getting a charge. Don't know the Ford wiring etc. on the newer trucks.

My service manual for a 99 Navigator with the same engine suggests checking the following:

Battery charge
Fuse(s)
power distribution box:
mega fuse (175 A)
in-line mini fuse (20 A)
fuse junction panel
Fuse 19 (10 A)
Electrical connectors
Electrical connections
Battery charge warning indicator
Other electrical systems malfunctions

Perhaps one of the fuses mentioned is the problem. I don't know if the Lincoln Naviagator wiring diagrams or component location is applicable to an F-series pickup, but let me know if you want them.....