Stick with preset numbers to control; the Mesa. In the Manual (JP2C) you will find a nice little graph on page 31 that gives you all different combinations. How it reads 1-15 gives you all the combinations then it just repeats 16-30: 31-45 and so on. If you have been storing changes on the Mesa you might have to redo one or two.
I did this for a friend running a JP2C with his FX8 and worked perfect, however with the MFC you might hit a few road blocks.
First things so everybody is on the same page Axe Fx and Mesa must have there own midi channels by default the Fractal stuff is on 1 might as well keep it there. Set the Mesa to receive on 2.
I dont have a MFC: Axe Fx setup any more, so this part I am not sure about. But I don't believe you will be able to run the MFC in Axe Fx mode. You can get it to work but with limitations (working with the Mesa Head that is) If it was the Axe Fx III would not be a problem. And in the case of setting up the FX8 with a JP2C, was no problem because it was designed with that in mind. So taking the MFC out of Axe Fx mode means, no tuner, no flying the preset from the Axe Fx.