Yes,

Take a look at the Gryration RF MCE remote it includes mouse actions as well. You can also get it with a matching keyboard.

For your first question, yes MCE is controled by a MCE remote and reciever and your tuner card is controled by its own remote if it comes with one. Another solution to this problem is software called Girder.

Your Pronto remote will learn MCE codes and you may be able to download the codes here. I would take a look at how others in the file area are handling the same problem you have.