I put a re manufactured alternator in my 2000 f150 with the 5.4 liter. Now all the lights flicker, go dim and then come back on bright again. I noticed when the lights dim, the heater fan speed also drops. The light flickering is constant and bad enough, that I can notice it in daylight also with the headlights on. It is really noticeable at night with the truck in drive (or any gear for that matter) sitting at a stop sign or sitting still in my driveway. I changed out the old alternator because it was making a loud chattering noise. I didn't have any trouble with the lights or fan with the old alternator. Why doesn't the battery volt gauge in my instrument cluster fluctuate all the time while it is doing this? It reads in the normal range all the time and doesn't move. The flickering lights are also noticeable at highway speeds, its just not as bad.

 

Put no credibility in the dash gage because it is a dummy gage.
The lights are flickering because the voltage is swinging from no charge to full charge a difference of as much as 3 volts.
Check the plug on the alternator for bent pins or not being fully seated.
Be sure the heavy lead nut is tight.
If ok, return the unit for replacement and have the replacement tested before you leave the store..
Good luck.

 

This is usually the voltage sensor wire (terminal "A" on the alternator's plug) having a poor connection to battery positive. It's like this on all Ford 3G alternators. These trucks have a rather cheap mega fuse block with rusty hardware in a brittle plastic base, so failure is guaranteed with age as you are experiencing. Mine broke in half when I tried removing the nuts. So I built a new one from scratch with A2 stainless steel hardware and a SOLID base. It will take a LOT of effort to break loose or become iffy.