Diesel Bombers - Fuel Issues on 96 F350

Hey guys, as you can see, I am new to the blog, so take it easy on me to start with. I have a 96 f350 ps with the 7.3 in it. 146,000 miles, and it gets driven about 300 miles a month. Not an everyday truck. I use it mostly to pull a 35 ft. tag along camper, but mostly it takes the trash out and children to ball games. Two fuel tanks.
About a year ago, not paying attention, I ran one tank out before switching over. It took a while to get it primed back, but after that, I thought it would be no problems. This is when the problem I have started. The truck starts easy even in cold weather (South Carolina, so not to cold). After driving it about 2 or 3 miles, it is almost like it is running out of fuel. It does shut off. It does eventually start back. After it warms up, it was no problems. So I started letting it run 5 to 10 minutes before driving it. At first, this seemed to correct the problem. So I thought maybe the fuel heater. Then right recently, it started doing the same thing even when it warmed up (after driving it 25 or 30 miles). After it warms up, when driving it seems to be missing. Similar to a gas engine not running on all cylinders. But usually, after a few miles it seems to pick back up and run fine. Here is what I have done so far.
Changed the fuel filter
Checked the fuel pressure (60lbs)
Bled the air several times
Switched tanks
I live in a small town, so most of my fuel comes from one place. I talked with several other diesel owners to see if they have any problems with fuel from this store. All said they have never had any issues with the fuel. I am just about at the end of my rope on this, as I am getting to the point that I am scared to drive it for fear of being on the side of the road. Any advice you guys have would be appreciated. Sorry for the long post.