I have big feet too and wear a size 49 in Sidi Crossfire TA's. I changed the OEM pegs out for a pair of Pivot Pegz and have no issues with using the shifter or the rear brake. The +/- rotation in their design enables my booted toes to get under the shifter with no problem without changing the shifter on the spline. It's not the least expensive option. but the Pivot Pegz deliver several benefits. They work great and the pegs are large and deliver fantastic grip and comfort while standing. Over the long-term they're supposed to enable boot soles to last a lot longer before needing replacement (which should save $$$), since a rider's boots don't have to move around on the pegs nearly as much. The pivot action prevents the need to shift feet on the pegs. I don't have enough experience to judge that fair wear and tear, but it seems to make sense.
http://www.pivotpegz.net/