Oh boy, too many questions at once. I can see this is your first ever refit and you're in over your head. I first suggest you spend a weekend reading the Camsoft install manual. I'd also read the install manual for your motion card. Is this a Galil card? And what is the model number. Same question on your I/O card.
Lets just do limits first. Many Galil cards, not all, have opto isolation on the inputs so you can use 24 volt. Check this out first. The galilmc.com website has a GREAT install manual for your card.
I wire nearly everything sourcing. I'd put the DC common (0 volt) on pin INCOM on the galil ICM.Then run your power out to the switch and the return wire back to your limit input on the Galil ICM. I'll tell you now this is backward from the default and you'll have to add this to startup.fil COMMAND CN 1,1
As you wire each switch have your control running and make sure you can see it change state in diagnotics.
The first refit is quite a challenge for anyone. READ READ READ and go slow.