The driveshaft is really easy to measure. Just measure from yoke to yoke as the truck sits level on normal ground. This will be your static length. This is what Tom Wood's will want. I have talked to him several times, thinking of what I wanted. I have a shop in Boise who has done several custom 4x4s around the Boise area and knew what he was doing. Was one of the first after asking what I building, not saying, "You can't do that with an Explorer!" Anyway, the driveshaft will be the LAST thing you will need to install. After getting your Atlas II installed, give them a call and he can walk you through exactly what he needs to know. Their turn around is usually only a day or two. You will have an idea after the truck is on the ground how much flex you will have and tell whomever is building the driveshaft and they can compensate for it. I'm having a long travel spline built for the front of mine as we speek.
Try to keep all of the yokes the same so your trail spare is just one u-joint. Unless you are planning on running a big V8 with HP and torque, I would stick with the standard 1310 U-joints. I have had great luck with them and that will keep a fuse in your system. A U-joint is a lot easier to replace then twisting a driveshaft, or broken axle, or...