Your results on the Commander, while not equal to ours, did bring to light some important points. With any aftermarket performance exhaust, a properly adjusted fuel tuner is critical. Likewise, adjustment of the stock clutch is sometimes necessary as well. This makes sense given the increase in power that is typical of a Muzzy exhaust system.
The Muzzy fuel programmer (Digi-Tune) is a very effective tool for adjusting the Air/fuel ratio. To say that it is "junk" tells me that you either didn't understand how to adjust it or didn't care to learn. The PC5 is also a very capable tuner. Both have pluses and minuses. In the end, it's really a matter of preference. If you want to go the more traditional cell based tuning method and create a "map" for your configuration, then the PC5 is the way to go. If you want a fast "injector load" based tuner that doesn't need a computer and allows simple "adjustment on the fly", then check out the Muzzy Digi-Tune. Muzzys offers both.