Peter,
On the X axis, I followed some instructions that was on the old IH site. I made the nut mount and loosely bolted it to the saddle. Then using my highly calibrated :}) digital caliper, made the lead screw parallel to the dovetails as I could. At this point, I tightened down the bolts for the mount. Next, I drilled the holes for the roll pins that I used to anchor the mount in one place ( see picture on my old web site:
My CNC Homepage ). Then the table was placed on the saddle, the gib strip put in and snugged down. At this point, the end plates were loosely mounted and using a socket wrench, we moved the table to one end of max movement and that end plate was tightened down. Then we moved the table to the opposite extreme and the procedure repeated.
The Y axis was done in a similar manner except there are bearings on only one end.
HTH