It's hard to explain without pictures but I'll try. Remember, I'm doing this with just a spirit level and a steel ruler. If I had a jig and a laser level I could probably get it done in 1/10 the time.
The first thing I have to do is determine whether the enlarger frame is plumb, level and square. Since it is attached to the baseboard, the frame must be square with the base. I could measure my frame relative to the base but every measurement subsequent must be offset by that amount which the base was not level.
The second thing I do is to level the carriage. If the carriage is not plumb with the frame, it will have to be made plumb. If the base is not level, the frame will not be level. If the frame is not level the carriage will not be level. If I have an offset toward level on the base, that offset must be carried over to the carriage.
Now, it is possible... PROBABLE, actually... that you will have some small error when you level your "projector's" base. It's not possible to get it 100% flat. That same thing is true when you do a 35mm projector. However, the first thing that must be done when installing a 35mm movie projector is to level it as well as you can.
You can adjust the lamphouse to be level, independent of the projector frame, but the better you level the base the easier it is to carry out your lamp adjustment and so on down the line.
Here's a story to illustrate my point.
One of the first theaters I worked at, I was being trained how to align a Dolby Digital sound system on a movie projector. I was trying to use a long handled Allen wrench to reach into the projector and make a critical adjustment without disturbing other components. My boss came over and asked, "What the hell are you doing?" I was flabbergasted to watch him take a screwdriver and disassemble the entire mechanism, align it piece by piece, from the ground up then make some final, minute adjustments in about half the time I had already spent fiddling on it (and still not getting it done.) He finished up and, with his thick Kentucky accent, he said, "Son, there ain't no use fiddling! If you're going to do this right you're going to have to break some eggs!"
Unless you know that your projector or enlarger's base is plumb, level and square with the frame, there is no use in trying to fiddle and tweak with the other components of the system.
It only takes a half a minute to level the base of your enlarger then to plunk a level down on top of the frame and verify that the frame is plumb. If it is, continue on. If all the other components are plumb, keep on moving down the chain until you find what's out of whack. But, if you don't, at least, VERIFY the basics you could end up farting around all day and wasting time.