Brief update. I did some cutting to test it out and the results were a little bit disappointing. I was getting a lot of chatter with light cuts in aluminum and it is struggling to climb mill. With conventional, it does alright, but it still has trouble. I could manage a .375" DOC, .01" WOC, at 20 IPM with a 3 flute carbide end mill. Before, the machine could handle .375 DOC, .035" WOC, at 25 IPM while climb milling without trouble. Usually, the spindle would start struggling before the chatter would kick in.
There was significant backlash in the Y axis. I could move it .01" easily just pushing back and forth lightly. I thought this was because of the ball nut so I took the nut off to look around. First, I noticed it only had 3 races compared to the 4 races on the other nuts I was using. I also measured the balls and they were .1540" almost exactly, maybe a little higher like .15403" but that last digit is nothing more than a guess with my micrometer reading to .0001". I measured the balls on the nut I was using for my X axis before and found them to be .1545". I swapped the old X axis nut in with the slightly larger balls and that made a noticeable difference. I could no longer move the assembly easily by hand and the mill seemed to get a little bit of steam back. It still has trouble climb milling anything much more than .005" WOC and 10 IPM. Conventional milling, it could handle .375" DOC, .02" WOC, at 20 IPM. At .025" WOC and 25 IPM, it chattered like crazy. I tried pushing it a little more with other cutters and playing with feeds and speeds, and using a 3/4" insert end mill, I could do .2" DOC, .1" WOC, at 20 IPM pretty consistently. It struggles the most when cutting with the Y axis positioned closer to me (away from the column) which I think is because of the unsupported section there. I am guessing that with it floating the way it is and supported by nothing but the rigidity of the aluminum plate, vibrations are aplenty. I am going to take care of the support there next to see if that makes any improvement. For that, I have a large 8x29x.75" piece of aluminum that will sit under the mill base and be secured in 4 points to the base and 3 points at the far end of the new Y axis base.
The other thing I think causing problems is backlash in each axis. With the dovetails, there was a good deal of friction holding everything still when it was stationary so the backlash from the ballscrews and bearings at the ends wasn't as noticable. With the linear rails and bearings, there is very little friction when stationary so the ballscrews, nuts, bearings, and motors have to do a better job holding it. I am looking into making them both a double nut. I also want to replace the bearings in the bearing blocks. The deep groove ball bearings provided with the ballscrews aren't doing a great job. One of them is making a knocking sound when rotated and they seize up pretty easy when I try tightening the lock nut on the ballscrew. If I can't get it to cut better, I think the next step would be to add 2 more bearings to the Y axis and either replace the rails (meaning the base and saddle may need to be remade, no big deal there though) or lose about 2.3" of travel dropping it from 7.5" to 5.2".
I was able to get it to make some decent chips, albeit a little slower than I would like. It was cutting for a little over an hour with a 3 flute indexible end mill. I drilled and tapped 6 holes in the table to secure a sub plate that I used as a jig to secure the part.