It sounds like the exhaust might be doing exactly what you said: resonating. It may just happen to hit the resonant frequency of your cab at those lower RPMs. Unless you hear rattling or it seriously annoys you, I wouldn't worry about it too much. A fix may be a different muffler or cat back system.
As far as the rough idle and stall, it seems like yours isn't as bad as mine was, but I had an O2 sensor go out on me, and the engine would stall when I revved it, and it would fluctuate a lot at stops. The exhaust had actually gotten hot enough to melt through my O2 sensor wires, you may have the beginnings of this happening. I would check along your entire exhaust and see if any wires are touching it and possibly melting.
Hope that helps!