Well, if you're going to the 700r4, you're going to either need to make it a manual valve body, get a constant pressure valve body, or install a TV cable. If you don't do any of these things, or adjust the TV cable incorrectly, you will likely burn the r4 up VERY quickly. So, make sure you definitely do one of these options.
You will also need a different (shorter) driveshaft. I don't know about you, but there are a few shops around me that will make a new driveshaft with all new U-joints for $200-400, depending on your needs and wants.
You will also benefit from an external trans cooler. There are plenty of options available, I just went with a Trucool 40k cooler after having a long and detailed chat with df2x4 on here. Heat plays a very big, if not the biggest part in killing transmissions. I've decided to go with -6 an line and hardware from Russell on Summit.
You will need to get a torque converter also. I can't help you much in this department, as I still consider them voodoo/black magic. I've heard of people swapping 4.3 converters in 5.0/5.7 GMT400s due to them stalling a little higher.
I'd also almost bet that you're going to need a different crossmember for the trans. I can't remember if the NV3500 has the same mounting points as a 700r4, but I'm thinking that they don't. I may be wrong.
Also, I'm not sure if your speedometer will work. I'm sure somebody will chime in with a definite answer and possible remedy if it wont.
For your last question.. while it were out, if it were ME, I would have it rebuilt with quality parts doing the typical "bulletproof" (and I use that lightly..) parts. I HATE touching stuff twice and wasting time. That's just me though.