jamis, your drone issue may be unusual. That Borla muffler and the Magnaflow are just about an identical design, and lots of folks have the Magnaflow without the drone. It's especially odd since you still have the resonators attached. I have exactly the same setup as you with that same muffler, and I have a short bed and regular cab. Everything in the exhaust system is stock with resonators with the exception of the muffler. I was very happy not to get the drone experienced by some with different exhaust setups...more often those without resonators. But...exhaust sound and the resulting noise can be very preferential, and some are much more sensitive to it. I can say with all honesty that when I'm going down the highway or cruising around town at a more or less steady throttle, I get no more noise than I did with the OEM muffler. It's only when I accelerate that I can hear the exhaust note, and it's not anywhere close to what I'd call a drone...instead it's a very pleasant sound. Even going down the road with the MDS kicking in and out, I get no additional sound different from stock unless I step on the gas.
Was your muffler bolted in or welded in? Did you go with the 19" muffler or something shorter?