If you can remove the upper manifold and get it back on without any problems, the fuel injector harness is easy to do. Several of the injector leads are hidden under the upper manifold.
The MAF wiring is an intergal part of the main computer wiring harness. See http://www.veryuseful.com/mustang/tech/engine/ for some links to pictures of both harnesses. There are several other diagrams that will be helpful as well.
Why do you want to change the harness? What sort of problems are you having that make you believe that a new harness would fix?