The Xylotex has terminals for the unused parallel port pins on it. You should be able to hook your home switches up to those, and not need the additional break out board.
As for E-stop, there are many different ways to do it. With Mach3, you can use another pin on the Xylotex to trigger a software E-stop.
So the Xylotex should be able to do everything you need, with nothing else needed. You might want to email Jeff at Xylotex. He's very good at answering questions, and pretty quick, too.