Is the pedal surface smooth enough for you?
I've got mine set up on an electronic bass drum pad. They have to be offset from center a bit. I'm sure if I hooked 'em up to my kit, the right pedal would be closer to the center than the left pedal.
Almost all double bass pedals are offset to a certain degree. Just the nature of the beast, I guess. I'm not sure if Yamaha's are offset more than most though.
Hopefully, they'll work out for you.