I also have the 900 classic, and this style bike is new to me, as is the heel/toe shifter. I don't necessarily hit the heel part of the shifter when moving my foot back, but I don't always get my heel correctly positioned on the heel pad. This produces non positive shifts. My shoe size is only a 7 1/2, and therefore I have to definitely move my foot from the front to the back. Basically I still prefer toe shifting.
Since I have only had this bike for about 2 months, I chalked it up to my needing alot more practice with this style of shifting. A friend of mine just doesn't use the heel shifter on his Harley. In another forum, I read of this guy in Canada who just bent the heel section out of the way, and another just cut that section off.
For the time being, I will continue to try getting used to shifting this way. I hope you will be able to work thru it, and enjoy riding your vulcan.