You can't just "not use the transfer case". The rear housing and output shaft on the 4x4 trans is different from the 2wd trans. Unless you plan on doing a 4x4, I would pass. I also read your plans for lowering the truck. I would not advise lowering the front in the manner you describe. While it will work, you will loose pretty much all of the suspension travel, and may end up with severe handling problems. A drop axle would be much better. Again, search the site for "Drop Axles", you'll find a wealth of info on who to contact and how to set one up. The rear should work fine with a flip, but expect to have to add a C notch to allow for axle clearance.
As far as hitting 50 mph is concerned, that can be accomplished with the stock trans. Running that speed for any length of time is another story, although i do it myself on a regular basis in 3rd gear with mine. 3.90 rear gears and 30" tires. It'll run it all day long, but runs better in overdrive (factory BW overdrive). That may be another option for you, as those transmissions are relatively easy to find.
