They are not integrated yet but these are some ideas:

One of the ideas was to use buttons as endstops and mount them to the aluminium something like this:

But since I also salvaged some of these optical interrupt switches from the printers it'd probably be a good idea to use these instead:

To be usable they require some more external components as described here (follow link for schematics) but the two essential resistors can also be fit directly on the PCB of the module like this:

With this modification I can feed the output of the module directly into the Uno without an additional board. Although I might make one to split the supply voltage for the three modules the final PCB for the the ATmega and the three StepSticks will probably have GVS headers for these endstops.