1. Vintage guitars are tricky. Especially when you aren't the original owner. You never know what kind of modifications have been done... unless you know exactly what to look for and exactly what you're looking at. The neck could have been replaced at some point and incorrectly installed... or simply the wrong width of neck could have been used. Or the neck that was used wasn't an original neck and the measurements of the neck aren't spot on... causing small changes in the way the strings sit.
2. The 3 bolt necks are more rare... They are also known for snapping out of the neck pocket... meaning there is a good chance it has been replaced or reset.
3. The string spacing is important on a nack as well. The nut is main adjustment point for misalligned string spacing... If the neck can't be moved from side to side... General the alignment is done by making a new nut that compensates the string spacing.
The Micro-Tilt system is for adjusting the neck tounge up or down... not side to side. I have a Strat with a similar ailment but it's not serious enough to have to do surgery... If you think yours is bad enough to have to put it under the knife I would do it this way...
Take the neck completely off the body. Plug the existing 3 holes for the neck with some kind of dowel rod or something similar... Apply glue around the sides so the rod stays in place. Next sand the excess glue off from around the plugs and even everything out. Next... You'll want to test fit the neck. you can use yarn... or guitar strings as the guide to see if its straight. Mark where the new holes should be. Drill them out and screw your neck in place. You should have a nice straight neck now if everything went as planned...
Good luck, hope you get your troubles figured out.