I have the same issue, I have the 3" extentions on my bike so my rod has an extender as well. I've adjusted it as far as I can and I wish the pedal was lower. I think I might look at modding the rod. or replacing it with one rod (shorter) instead of the stock rod with the extension that came with the kit.
Rides:
2003 Suzuki Volusia 800 (too small, sold)
2005 Yamaha Road Star Warrior 1700 (Awesome - medical reason forced sale
(Unfortunate, Unscheduled, Car Induced, Violent Bicycle Dismount)clicky details)
2006 Suzuki VStrom 1000 (GREAT deal forced trade)
2007 Yamaha FJR AE 1300 (FJR: Freakin Japanese Rocket)
"The nine most terrifying words in the English language are, 'I'm from the government and I'm here to help.'"
Ronald Reagan Go STEELERS
(and anyone playing the cowboys)