ExNews4XJ has some good info there. The bread truck motors were designed to replace the small block 350s originally placed in those trucks, and are in fact nearly a bolt-in swap from a 350 to the 3.9 diesel. Those trucks are pretty hard to find though unless you know a place that auctions/sells commercial surplus and used vehicles; they tend to be bought up quickly.
I recently finished a 5.9 cummins swap into a Ford Bronco. Sparing a lot of the technical details, one of the mods we did was to remove the in-tank fuel pump and plumb the tank directly to the input on the fuel primer of the Cummins, and this worked great. Definitely hook up the return fuel line if you do this - the Cummins pump has a fuel heater after it to reduce gelling, and they purposely send excess fuel back to the tank after it goes through this to help heat the rest of the fuel supply.
Aside from that, the 5.9 (and 3.9) motors are purely mechanical. At least before they went to the 24v versions. We had the motor installed and driving with just two wires: one to open the fuel valve solenoid (consider this the same wire that activates your ignition coil) and one to hit the starter solenoid. The mechanical controls on the motor take it from there. We were able to wire up all the factory Ford gauges in the Bronc to the Cummins unit as well - oil pressure we cut and spliced because the sending range was the same, engine temp we used an NPT adapter fitting to fit the Ford sender, and we got a tach signal by remounting the Ford tach sensor and grinding additional notches into the Cummins harmonic balancer. If you modify the tank properly you can keep the fuel level sender fully functional. We even used a standalone "computer" from a '90 CTD Dodge pickup to use the intake manifold temperature to properly trigger the intake grid heaters - which used the Ford factory 'wait to start' lamp. This same module also gets input from the 'water in fuel' sensor and activates the factory lamp. Pretty pimp to see the whole thing work from in-cab.
The power steering pump on the Cummins motors (which is usually an OEM unit adapted to the Cummins geartrain) bolted right up to the Ford/saginaw power steering box, so that's a non issue.
Alternator...we ended up using a heavy-duty adjustable unit from a school bus. The alternator on the Cummins motor was regulated by the Dodge computer, so if you're lucky enough to score a Chevy-based bread truck motor, you may get an internally regulated alternator.
We used the factory vacuum pump on the Cummins motor, and t'd it into the vent control lines and brake booster line. All accessories work fine.
Not sure how much of this helps you, but feel free to reply/contact me if you want any more info about Cummins swap stuff. Here's a pic of how it ended up...pretty clean IMO. Used the Dodge radiator and intercooler too.
I'd love to see someone on here put one in an MJ.