end stops for milling will be problematic, unless you make them movable. you can use your software to jog the system around, since the lcd can be a bit hard to get it jog one step at a time. you will have to reset the z on each tool change, unless all your endmills are exactly the same size. it would be easier to set zero then line up your piece if you are only using sd card. endstops on a mill will screw up your toolpaths if you dont remove them after the milling starts. when it comes to printing, however, endstops are almost a neccesity.
and as far as auto-homeing is concerned, youd need to have all 3 endstops in use in order for it to work. now you can use the lcd to set home and it will return to that position automatically if you use the home command (not autohome)