Dan, I am unsure what you mean when you say that the plumbing is 3' above the floor. Most basement plumbing is either up amongst the joists or under the concrete. There might be a couple of pipes coming down from the area under the first floor to under the concrete, but normally the plumbing is pretty well out of the way.
In any case, if you can get a source for Family Handyman magazine, there have been several articles over the last couple of years that deal with various aspects of plumbing a basement bathroom. They have great pictures and offer alternate methods of doing things depending on cost and other considerations. The pictures are a great aid in helpingn you understand what is involved. Henry