Mike-
You need to be a little careful with the 'stall in a known position' type of reference. I used to work for an OEM that used this method in several applications. Every once in a while something would get into the axis path or the powertrain would get a little dirty, etc. The axis would stall before it reached the rigid stop it was supposed to reference against. The next controlled move after that reference was usually something to behold. It sometimes ended in a god, solid, high velocity crash into some machine member.
I'm not saying this is a bad reference method. I still use it myself. Just be aware of the possible consequences.
Keith