That is something I would definitely do, that Y travel gets eaten up pretty quick!!
Its much easier to do now than after everything is mounted.
BUT now that I think about it if you didn't already order the extended ballscrew from cncfusion with your kit then its kind of a moot point.
Maybe Michael will send you an extended ballscrew that is drilled and tapped for a bolt and washer in the free end of the ballscrew, that will also keep you from popping the snap ring off the end, it is definitely a more positive stop.
And as far as limits, personally I dont use them on my mill, the steppers will stall before anything breaks, I use home switches on each axis, and then just set up the soft limits in mach 3. It simplifies the mess of wires
as there is not much room on these little machines.
Then you just home the machine and turn the soft limits on and your set.
Have you seen
Creavice Reamer's site
OH and are you using the nema 23 620 oz for the Z?
Here is a link to my
SX3, wont be much help to you as I did not document very well, but might give you some ideas.
JTCUSTOMS