My biggest problem has been alternators. I am now on number 5. No one seems to be able to figure out why they all have failed, (except one had bearing failure).
These trucks, (when equipped with the turbo diesel) are notorious for automatic transmission failures at around 40,000 to 60,000 miles, but I am just now beginning to see some shifting problems at 160,000 miles. Ford engineers should be flogged for installing a commercial truck engine rated for up to 35,000 lbs GCVW, in front of a wimpy car transmission. They can talk up the E4OD all they want, but is is still just a car transmission. I have spent much time researching adapting an Allison Automatic, (the only real truck automatic transmission ever invented), but since my truck is a 4x4 this is not a bolt-in option.
I am now beginning to notice some front axle suspension components are wearing out. I'm not looking forward to paying for those repairs, although the Hotchkiss Live axle system is cheaper to repair than the crummy independant suspension systems used on other trucks.
This truck was a terrible kidney buster until I replaced the tires and shocks with aftermarket items.
The engine has pretty bad turbo-lag coming off the line, but it makes up for it in mid range power, (which is astounding). My truck as equipped weighs 7,200 lbs, but can whip most other trucks of much lesser weight and keeps up with cars nicely. When traveling the steep North-eastern Arizona mountains, I set the cruise to 70 or 80mph and I am passing absolutely every machine on the road, (without shifting out of overdrive)! I mean corvetts, Z28's, Dodge V-10's, everything!! It takes the curves like it's on rails and doesn't slow down for any mountain grades.
I love the super heavy DANA-60 front axle which has now been downgraded to a DANA-50 on the '99 and newer trucks.