I have a '06 with 5,500 miles.
It has been in the shop 4 times for turbo problems, and let me say this, I have owned Fords for 30+ years, this is my first diesel and I love it, but this is the first one I have ever had I have had to take back to the dealer for any kind of problems.
Anyways,
Came from the dealer with the "Extra heavy duty alternator"
Never had to replace the batteries or alternator.

When driving down the road, if I go over a bump, the battery light comes on. Go over another bump, it goes off. Sometimes driving down the road, it will flicker on and off.
Can't seem to find any loose wires or cables any where, batteries are showing good voltage, and when the engine is running whether the light is on or off, they are charging.

Any ideas before I have to take it into the dreaded dealer?

 

beforeiforget761,

Sounds like you either have a loose or chafed wiring that is causing the intemittant problem.

Did they finally get the turbo issues fixed and what was wrong with the turbo?

Sounds like you may want to find a dealer with a better and more qualified 6.0 diesel tech.

What mods if any do you have on your truck?

 

Yes, the turbo problem has been fixed.. The pipe coming from the turbo to the intercooler kept poping off all the time, and it is finally fixed (as of now).

The only mod I had was a air-raid cold air intake, but once I started having turbo problems I took it off. It hasn't been on for the past 700 miles or so.

Other than that, Just a 5th wheel hitch and a trailer light connector in the bed (connector was installed by ford)

 

Check the alternator plug. They sometimes dont lock down properly, push down on it, If you feel it click, you found the problem.