[machinechick]

The y really can't be adjusted, you could use shims, but you really shouldn't have to, that axis and the column to the base should be good from the factory, if they're not, you could return or start to scrape flat. Check for paint, or a burr, just like you did for the column/base. Also make sure that little set screw on the side of the head isn't introducing a twist to everything, and that the boss on the saddle didn't get dinged during the move. Here's some photos of the mods. Putting the two bolts on top gave me more leverage above the pivot boss which allows me to tram y much easier, the self leveling washers help to evenly distribute the pressure and press the head casting flat against the z-axis saddle. (at least thats how I'm thinking about it). In retrospec I also think this mod makes the head/saddle attachment more rigid, I also think getting some quality teco or gibraltar bolts wouldn't hurt.