I'm in the midst of realigning my Besler 23C-II. I've got nothing more than a spirit level, a steel ruler and a piece of SMPTE PA-35 test film.
http://www.thedigitalbits.com/articles/robertharris/smpte35pa.jpg
It's probably going to take an almost complete teardown and rebuild but I fully expect to get near-perfect alignment out of it when I'm through.
Regardless of the tools used, this is a job that just requires time and patience and a steady hand.
I have done similar jobs on over a hundred 35mm movie projectors. To be blunt, an enlarger is not much different than a movie projector. Think about it for a second... An enlarger is nothing more than a projector. It operates vertically instead of horizontally and it only projects one frame at a time. But it's got a light source, a film trap a lens and a projection screen. It's just a specialized version of a projector.
From what I can tell, so far, aligning an enlarger is almost the same. You can use test jigs and lasers to align them but, when it comes right down to it, you still need to do it by hand. You need some tools, some patience and a lot of common sense.
The first thing you do is level the base your projector sits on. If its not sitting level, nothing else will work right. You could work for hours and hours but still not get it right unless you start with a level base. Then you align your lamp, your condenser/diffuser, you film trap, your lens and your easel until they are all centered, plumb, level and square.
I really can't explain it to you. I don't know of any manual that really gives the full detail on how to do it. You just have to see it done once or twice. After that, the best thing you can do is to get your hands on one and figure out what makes it tick.
It might sound like a PITA but, if you have ever watched a movie at a top-notch theater like the AFI Silver, you will appreciate the difference.