In your schematic you can safely remove the pull up resistors connected to the Port 1. When you write "1" to this port to make it as a input port, there are strong internal pull ups in MCU which get switched on.

Never plan to connect any long wires that lead to limit switches or other such devices as you are asking for trouble due to noise pick up . For this reason an isolation very near to the MCU is good.

And as to the outputs, Erik has already warned you. Better to always use a buffer here.

Raghu