For the most part, they are pretty similar. Dodge makes a good motor, and with a manual trans you should be fine. The 7.3 PS motors are great too, not industrial rated, but good.
The 98.5 and newer Cummins have a flat power curve. It gives max power for a large range of the curve, it is designed electronically to do this. The previous cummins was not as powerful, but still a good engine. The automatics are derated to a lower torque rating than the manual trucks. The older 12v engines with a manual put out similair power and are still good engines.
I personally like the Dodge styling better than the Ford, and I like the interor better. Have a fun truck hunt.
Oh, if you plan on running bio diesel, you should check with Ford and Dodge about their approval. Some of the fuel lines and seals will need to be replaced with Viton in some of the older diesels. Bio diesel doesn't put out as much power as regular, but bio is chemically a lubricant and fossil diesel is a solvent. This means that if broken in properly, the bio diesel engine will last longer than the regular diesel engine.
If it were me, '99 Dodge Cummins, 4x4, ex cab, short bed. Detroit in the rear, truetrack in the front with 3" lift and BFG AT T/As.