[Titaniumboy]

x axis,
1. right, the holes aren't critical. .256 is standard for 1/4 socket screws, you can make them to fit whatever screws you wish as you noted you'll drill and tap for them in the endcap.
2. 1/2" is fine if you then take 1/8 off the length of the standoffs.

y axis,
1. the holes can be larger just like on the x axis, just for mounting to the base, stock holes are for M6 screws but can be tapped out for 1/4-20.
2. the bearings should be slip fit, the 26mm bearings are technically 1.0236 dia. could go to 1.025 bore and be fine.
3.You can rough out the bore with an endmill and finish with the boring head with the cutter pretty close to flat on the bottom.
I actually bored mine on a lathe with a 4-jaw chuck.

Hoss,

Thanks for the help! I finished up most of the X-axis stepper mount on Tuesday and I just have to enlarge the .75" diameter hole I milled with an endmill up to the 1.024" diameter needed.