The spindle carrier and spindle sounds to be in decent condition for its age. Incidentally what sort of reading do you get when you put a DTI plunger onto the spindle and revolve it ? Try it with the spindle fully withdrawn and then fully extended.
A deviation of 0.025” in 20” of spindle travel along the master way sounds a lot to me. I would be expecting the deviation to be in single figures at the most. Are you 100% sure that the spindle didn’t revolve slightly when you were propelling it out. Obviously that would affect your reading In a big way. How thick was the shim you put in between spindle frame and column ?
Regarding the ways - I’m not familiar with that make of machine but over here on the machines of that age the long travel box ways came with two methods of guidance. One method had the saddle being guided solely by the front way. The “ Fast Angle “ of the saddle rode on the inside face of the front way. That’s why we used it as the master way. The saddle was kept in contact with the way by use of gibs bearing on the front face of that way. It’s called “ The narrow guide principle”. So all the work was done by that way.
Later on that changed. The fast angle still rode on the inside face of the front way but the gibs were moved over to the inside face of the other way, the one at the rear. I think this is a better method, especially when the long travel ball screw is positioned in the middle of the two ways. Imagine opening a cupboard drawer with both hands, that is the new method. The old method was like trying to open a cupboard drawer with one hand.
Which style of way does your machine have ?
How big a job is it to tweak the column over to correct the “ spindle in line “ reading ? I would presume it involves pulling the dowels and loosening the holding down bolts.
On our machines there was a rib about 3” by 3” cast onto the back of the bed. This was machined in line with the bed ways when it was all being planed or slideways ground in the shop. This worked in conjunction with a setting strip on the back of the column at the bottom. The setting strip was machined first and it was used to sit the column down on it’s back when the column ways were being planed or slideways ground. So everything was in line. The column was pulled up to two 5/8” thick plates inserted between the rib on the bed and the setting strip on the back of the column. There were two bolts that went through the rib on the base and into the column via the two plates. You could use this system to adjust the “ spindle in line “ alignment. As time went by and differential wear appeared in the spindle frame/column fit we used to remove the plates, surface grind them, and replace them. On a machine that was well used, maybe double shifts with a lot of milling, this procedure would take place every 4 or 5 years.
Does your machine have a similar system or is the column just sat on the bed ?
What worries me in this story is that someone inexperienced in Hor bore work in the past could had altered several alignments incorrectly just to get the machine working after a fashion. Doing several ” wrongs “ to achieve a “ right “. It’s easy to start chasing your tail if you don’t know what you’re doing. Hor bore alignments need a lot of thinking about. Spindle only machines aren’t too bad, the one’s with a built in facing slide are much more complicated from an alignment point of view. You have two entirely different methods of generating machined surfaces In one machine.
I hope that all makes sense. Some photos of the relevant areas of the machine would be a great help.
Regards Tyrone.