Measure out your distances first only as a starting point. Then, assuming you can do the phase switch easily I'd do it next. Throw that disc I mailed you in and run the phase track over and over. Get things as right as you can that way.
Then, throw a little time alignment on it again. If you can listen to JUST the tweeters or JUST the mids or midbass drivers on their own (in pairs) it's MUCH easier to tune that way I find. I play the number track (counting from 1-25) for that one. The TEEN's and Twenties are great for tuning the tweeters since there is a little more HF
content. Do them individually and you'll get a rock solid center.
If you have trouble getting a center you might try changing the phase of one of the drivers. In fact, that's what I'd look at first if it gives you trouble. Hopefully you can do this all from the computer or you'll want to pull your hair out.