grinderdust,
Have fun on this one, as I found out there seems to be no true spec on this one and you will need to measure. Having said this, there is some play in the bearing caps so you can do some final adjustment.
As to alignment, industrial hobbies (if it is still up) has an excellent tutorial on how to line up the ball screw. Basically you get it parallel to one of the dovetails.
If you are going to make a new holder, I suggest that you make the "legs" longer so you can also pin the nut to the saddle. (see pictures on my site http://bellsouthpwp.net/A/r/Arts_home_page/cnc/ ) to see how I accompolished this. NOTE: this is where the round column came in real handy:})
I also have a cad "working sketch" that I can send you with all the dimensions etc for the conversion that I did.
Art
AKA Country Bubba (Older Than Dirt)