First off it is pointless to tap the pegs for the bolts because they are cast aluminum and will eventually fail or just break off.
The Boards I sold came with stainless steel 1/4-20 flat head bolts 1-3/4 inches long, an aircraft nylon lock nut for each , along with a nylon spacer that fit into the recess and the bottom of the peg to allow the nut to sit "on top" of the bottom the peg itself. If you use a longer bolt it may hit the brake lever on the right.
Out of 200 plus sets sold only one customer found he needed to reposition the brake lever , as his was adjusted too high and hit the bottom of the peg.
Normally I would not suggest tapping any aluminum to hold a bolt that is to basicly hold the weight of the rider unless you have at least an inch of material to work with. The added vibration from the bike along with the stress involved daily really calls for the use of steel to steel fasteners.
I am not aware of any issues regarding the shift lever other than those with extremely large boots having to re-train themselves on moving their foot to transition from downshifts to upshifts.
I can not give any advice on the Kury boards, but I think it is you kawabungie that should post photos of the problem you are having as I can not offer help without more info.