Thanks to all the info available on this forum.
With the lack of limit switch inputs on the 6040 I decided to buy a upgraded breakout board with the extra inputs.
You beaut, the new board arrived needing a few mods to make it work so I removed the old board ready to replace it.

Upon closer inspection there are inputs on the existing breakout board for limit switches.
You can't see them with the board in place, you must remove it and inspect closely.
So after some customised switch mounts and strikers, a few clicks in ports and pins she is running sweet.
Even got the work offsets figured out to run the existing programs Ive written.

Once again thanks everyone for your info.
P.S. I have a brand new breakout board going cheap, never used. hehe