I see where you are going with this.
Look around the internet. You can find rotary counters that are designed to do just this. The usually involve a slotted wheel that goes on the shaft you are monitoring, that pass through some type of sensor (usually IR, sometimes a Hall sensor). The sensor would then be tied to your system (I would recommend using spare pins on JP4). Spin one direction and you step up a counter. Spin the other way, and you count down.

The only trick is knowing where to start. You would probably zero your print head, then initialize the counters for the tracker.

Your other option is to use metal gears for your drive system, then you really don't have to worry about slippage/skipping.