I agree, just look the boot over good and make sure it doesn't have any rips or holes in it and if it hasn't, reuse it. I would say that since the driveshaft and other parts are in the condition that you described, that it would be a good idea to go ahead and replace the u-joint because it's probably in bad condition too. If you don't replace it now, while everything is apart, you will just have to replace it later.
Most 4-wheeler problems are caused by a loose nut connecting the handlebars and the seat!!
You only need two tools in life -- WD-40 and duct tape. If it doesn't move and should, use the WD-40. If it shouldn't move and does, use the duct tape.