Nice project you have going on. Luckily for you you have a Dodge engine. From the other thread you were posting in, I thought you had an Industrial engine. I'll dig up the wiring info you need to get the engine running. Here is a link to some wiring info. Post #3 shows the ecm wires you need to hook up to get the engine to run stand alone. If you don't have the OBII connector and wiring from the dodge dash loom, you'll want to get one and add it in. That way you can check codes, and load a tuner/programmer if you would like to.
http://www.competitiondiesel.com/for...ad.php?t=96752
Yes, you can get the engine set in the truck, hook up the wires needed to run the engine, and terminate the un needed wires. Your ECM incorporates the body harness wires and engine harness into one plug. As long as you leave the engine harness in tact, there shouldn't be any issues and that is a pre emission engine unless it has egr, so you should be fine there as well.
I like P-pump 24v's, but I have grown to like the VP's too. I'd leave it VP unless you want to make 550hp or more. The big down fall to the P-pump swap is the lies. It doesn't seem to matter who bends them, they are prone to cracking. A set is $650 or more and you'll want to have a 2nd set if you plan to drive long distances. Not many people stock them and it'd be unlikely to get one if one cracked in the desert etc.
You can call these guys and see of they'll do your harness, but I'd honestly save the money and do it your self. Then you know what you have when you're done.