If you are going the 7.3 route, there is the Powerstroke and of course the IDI. Not a whole heck of a lot goes wrong with either version. If you want a simple and reliable old engine, can't go wrong with the IDI. Definitely try and find a turbo 7.3 IDI. The additional power is a nice touch from the naturally aspirated one. By no means are they power houses though. Just a good ole reliable engine that is simple and easy to repair. A 7.3 Powerstroke on the other hand makes a significantly better amount of power. Of course the power didn't just appear and there were many technological advancements to achieve an increase in numbers. Because of those advancements there are more avenues for failure and they are a step more complicated than its IDI predecessor. Again, though, not a whole lot that goes wrong. Main problems are leaks that need to be properly diagnosed so you don't spend unnecessary money. The injectors on the Powerstroke are nearly bullet proof. Like any injector, they won't last forever but they are incredibly durable in terms of what can be run through them (metal, dirt, etc.) and they continue to actuate properly. Both 7.3s share nearly the same internals and major components because the IDI was the starting base for the Powerstroke. That being said, it doesn't mean parts are interchangeable. In many cases they're not and have slight variations that prevent them from working. The 7.3s are just solid engines, IDI or Powerstroke, and with proper maintenance can easily see 400,000-500,000 miles. I'm not as savvy with the Cummins 5.9s (always been a Ford guy, but try to keep up with all diesels) but I do know they are both reputable engines. I have heard that the 12v is more reliable than the 24v, which makes sense because there are less moving parts. Power-wise I would assume the 24v is ahead there because of the improved airflow via the additional valves. Cummins has made a name for itself in the reliability world of diesels and I have seen many chalk up similar and sometimes higher mileage as the 7.3s. Both versions of the 5.9 are fairly simple and easy to work on until you get deep into the internals with the 24v. Just more going on inside of it. Another nice thing for the 5.9s are the amount of space you have to work with under the hood. An I6 is much easier to work on than those massive 7.3 V8s. When doing more significant repairs, there is less that has to be removed or maneuvered out of the way to work on the part you are replacing/repairing. Truck-wise, I would personally prefer the Ford. From my experiences they just seem to build the better all-around truck. 90's/Early 00's Dodges just seem to have automatic tranny woes. 90's Fords (especially the E04D) also seem to have automatic tranny problems. Dodge or Ford I would try and stick to a standard for reliability or an automatic for drivability. I see your 6.9 is a 4 speed, so if you don't mind owning a stick I would try and find one just because they tend to last longer than the autos. Like everything I post, these are just from my own experiences/knowledge/and opinions, so I'm sure there are people that will disagree with me. Hope this helps in your search though!
P.S.~ I have always used powerstrokehelp.com . Bill also has a YouTube channel that is a fantastic resource for any Powerstroke (7.3, 6.0, 6.4). Gives you TONS of free information that is not only from a reliable source, but also from hundreds of experiences. I know you're timid of the EGR engines, but if the proper steps and maintenance are taken they can become fantastic motors. 6.0s make some incredible power and aren't too bad on fuel if you can keep your foot out of it. I just love the way they sound (from Jet to Chewbaca) That's something I didn't really touch on before, but it's pretty obvious the I6s will do better than those large V8s. You CAN see 20+ out of either, but regardless the Cummins will get better mpg.