I'm going through the same at the moment. Bad vibration under under braking especially at speed,which can be felt through the brake pedal. I had this last year but it was sorted after I changed the front disc. This time the first thing I did was to change the back disc....still the same. Changed swivel bearings,checked regreased & re-torqued hub bearings...no change. New pads all round (getting desperate now) & it's still the same. I've even got my DTI out the make sure my front disc had'nt warped in the year but they're spot on.
It's the fact that you're actually getting feedback coming up through the brake pedal that makes me think it's brake related...but i've run out of bits to change on them now.
I'll keep a keen eye on this thread!