I have a '99 F350 Crewcab PSD 4WD. The past week, I've been having to jump start it every morning-and sometimes even 4-5 hours later. Had one obvious bad battery-so replaced it and still having the problem. Started thinking alternator-but it shows its charging when running, although when starting it up, gauge shows it not charging for a couple minutes, then slowly it comes up. After it warms up, test leads on battery shows 13.5 volts-so it is getting a charge. Had both batteries load tested-they were okay, although the old battery I still have in there was really warm when we pulled it out today (3 hours later after truck ran this morning). Had smoke/steam coming out of cells when we pulled the caps and I've noticed it has a gray spongy looking material in each cell along with the acid. Never seen that before. Local NAPA and CarQuest can't bench test this alternator-don't have the right leads, terminals or something. Ford dealer can't either-says this alternator is not serviceable-can't replace regulator/brushes. They're telling me to bring it in for $150 diagnostic test, and if it's the alternator, that'll be another $284. Anyone else got any ideas? I still don't like the battery being so warm, but NAPA load tested it (if they did it right) and said it was fine.

 

I don't know exactly how the two batteries function in your truck. Are they in parallel for starting? I wonder if the new battry is dumping current in the old one. Something is causing it to get hot. If you could get ahold of a clamp on DC ammeter, You could start out from a cold engine and check charging current to each battery.

As for the alternator, for $280; I would be willing to spend a lot of time making brackets for a different type. You might load test it by adding old headlights across the system to see if it is putting out rated current.