I have worked on both engines when I was still working at the dealer. I would not own the 4.0 SOHC engine.
It amounts to this;
The 3.0L has less to break, is easier to work on if the need does arrise.
The 4.0L makes more power, but is harder to service and I have seen several cam and timing chain failures which led to catastrophic engine failures. All were just out of warranty, although none really looked all that well maintained.
The 3.0L most likely will get slightly better but similar milage, that will depend on your driving. I would most likely get better milage out of the 3.0L, but if your heavy footed, they will be close.
If your goal is to have a fast truck and use it for towing heavy loads, the 4.0 may be for you.
If you plan to keep it for a long time and don't care about a few less horsepower and want some peace of mind reliability, go with the 3.0L.
I would also only buy the manual trans, I am not very fond of the 5R55 trans either. In my opinion it's too light duty for the application, and the manual takes less horsepower to turn.
For those of you who are taking votes on the all around longest lasting engine, I would have to say it's a toss up between the 240/300 Ford 6 cylinder, and the Chrysler 225 Slant 6.
I just sold a 1988 Ford van with it's original 300ci six cylinder, with nearly 400,000 miles on it and it's still going strong.
I would also have to put the 2.3L OHC in the running too, but the 300 is a much stronger engine that requires less maintenance and makes more power.