Just going by the seat of my pants (I don't have my bike nearby), I'm pretty sure you can remove the bolt through the shifter arm, rotate it in a manner that you'll get more clearance between the peg and the shift actuator, and replace the bolt. Looking at the parts diagram:
, it looks like there might be a rod that you can adjust. It runs from the shifter to the actuator (I was thinking of my KZ in the strike-through above, it's a direct attachment IIRC). just loosen the nuts and turn the rod. If both ends have the same style threads (both left hand or both right hand) then you'll have to take things apart to actually lengthen it. This should gain you some clearance using the stock arm. I'm sure someone will speak up if this won't work and/or won't help.
For the record, I wear size 13 work boots when I ride and can't say I've ever had trouble. I'm not saying you're doing something wrong, just that I'm riding a stock bike and have clearance as it sits. Your shifter may be in a different place from the factory, I don't know.