I noticed that the Mesa Boogie Mark III is not listed as one of the compatible amps for the mini amp gizmo, as well as the standard amp gizmo, is there anyway to set one of these up for the Mark III?

Actually, you can use either. There just isn't a special cable listed for the amp because it uses standard 1/4" plugs. A regular Amp Gizmo is recommended with a Mark III - Since the Mark III has one footswitch on the front panel and two on the rear, the Mini Amp Gizmo's 1/4" adapter cable can't reach all three jacks without modification. The Amp Gizmo has individual 1/4" jacks, and you can use them to run individual 1/4" cables to each of the footswitch jacks.