[mr48chev]

Almost every part of the trucks has been reproduced somewhere including whole cabs if you are inclined to go that way.

I'd have to first say don't pay a lot extra for things that you aren't planning on using. A fully rebuilt stock six is great if you are buying the truck to restore to showroom original but is something you will have to try to sell if you are planning on putting a V8 in the truck from the start. Paying many $$$$ extra for that may not be prudent though unless the rest of the truck is so perfect that it makes it worth it. The same for wheels, tires and everything else that you most likely don't intend to use.

As far as rust. The floorboards especially on the drivers side and the kick panels are one area to check.
The cab corners commonly rust out but replacements are fairly inexpensive. Also check the area around the lower door hinges and the bottom of the front of the cab. Another area is the seam around the back of the cab on the belt line where the roof joins the back. That seam also is a rust item and is probably the hardest thing to deal with if it is real rusty.

Check the frame for rust damage and more for bad modifications. I've bought several AD trucks over the years that had real butcher jobs done on the frames to install engines wouldn't fit otherwise. Welded on brackets for rear bumpers or trailer hitches don't really count as they can be cut off and cleaned up.

Three or five window cabs are personal preference for most of us and add in which is available at the time we are looking for a truck. Original transmission only counts if you are going to keep the truck stock and one doesn't add or detract from the value of the truck but for a restored truck I'd think the three speed might be a bit more desirable then the Granny shift 4 speed. The main thing is get the best cab and frame you can get if you intend to use the original frame. If you are intending to restore the truck to original get the most complete truck you can find wiith original pieces on it. If you are going to put a V8 and automatic in it the condition of the original engine and trans isn't an issue.