Non-Standard Paralel Port?

We have some existing old hardware that is using some odd setup for paralel port pinouts. I am wondering if it would be possible for me to set these up to plug and play with emc2? The drives are 4 axis and use 2 paralel ports, one port-two axis. The step and direction pins are not to much trouble they are on pins 2&3 (1st axis) and 6&7(2nd axis). The problem is the limit switches are on pins 1&14 (hi&low 1st axis) and 16&17 (hi&low 2st axis).

Is there any way to use these pins as inputs with emc2, or am I going to have to make my own cables to cross them over to some other pins (like 10-13)?

I know, hence my problem. The original Dos software running on these machines now, is using the 4 pins that EMC can only use as outputs as inputs.