Mine is a '93 F250 NA 7.3L ext cab 4x4 ZF5 w/D60 swap and I love it. It had 4.10 gears when I got it, and thats best for hauling and working in the woods, but this is also my daily driver so I swapped them to 3.55s for the better fuel milage. I would stay away from the E4OD. They die at around 125K~150K, and cost $2500+ to rebuild. C6 is cheaper to rebuild, but I think you have to go back to '92 to get one. The NA 7.3 isn't a power house, but it's okay. Throw a turbo on it and open up the exhaust, and it really comes alive for you. It's not needed, but if you do a lot of hauling over the road, it is worth while.
On the older F250 diesels, the only difference between them and an F350 is the front axle. The F350 has a Dana 60, and the F250 has a Dana 50 (TTB) unless it has been swapped out to the D60. The D50 is up for the task, but more expensive to maintain, and IMHO the ride isn't as smooth. Either way, I wouldn't limit your search to the F350. The rear axles on these F250/350 diesels are rated for over 6K lbs. I made side rails for my bed that allow me to stack all the way to the top of the cab. This makes 1 full cord and generally weighs around 5K. The overloads still have about an inch to go on them before they bottom out.
Not sure how familliar you are with older ford 4WD trucks, but I would recommend that you go through the front end completely checking seals, U joints, ball joints, bearings and such. I got mine from Jacksonville FL in '09. On the up side the body didn't have much rust. On the down side, sand had eaten out every seal on the front end which has caused me recouring problems ever since. I had a D60 put in this fall and I'm REALLY hoping that stops the problems
If I had the money when I got the truck, I would have done this to begine with. I had just come off of a 6 week layoff and we had just put a new tranny in my wifes car, so I was in a mode where I was just fixing what I had to in order to keep it on the road. Over the course of 4 years, it would have been MUCH cheaper to have put the D60 in to begin with.
At the end of the day, wait for what you want. If the IDI really trips your trigger, I would highly recommend the forum over at oilburners.net. They have a group dedicated to the 6.9/7.3 and those guys have forgotten more about that truck/engine than most people ever learn.