My feeling is that you, the mapper, ultimately get to decide how to handle a map that's internally inconsistent. In many cases, it gives you a chance to be imaginative and artistic since there's often not a perfect way to do it.
In this particular case, I would personally handle it either one of the two following ways:
1) Align all the horizontal doorways for starters. In order to avoid rooms colliding with one another, I would also try to keep a certain minimal amount of vertical space between any two sections (probably the same you already have). Since the various sections are already not connected vertically, inserting vertical space would make bigger gaps between elevator stops so I'd use either lines or arrows to connect them. Or maybe fill in the gaps in the elevator shafts with the level tiles to give the impression of continuity between stops. It wouldn't look too out of place but it wouldn't be completely accurate since you're adding a bit of stuff where there isn't any.
Or...
2) Keep you maps generally as they are since keeping the sections themselves aligned and not the doorways make the maps more orderly. I'd simply add in line or arrows between elevators tops and *also* between doors that aren't on the same level. I can't explain to you why I *hate* using letters or numbers as connection points on maps but I just do. In my mind, it's only acceptable for RPGs or similar games where connecting points between areas are not on the edge of a map where you could use lines or arrows without overwriting the game's graphics. Of course, adding so many arrows and thus adding horizontal space between rooms might not look that good either, but I assume that if I had to make a choice, I'd then stand by it, good looking or not.
In any case, lines or arrows would definitely be preferable (to me at least!) when the sections are far apart, which happens in a major way in the Great Palace.
As for what the best layout would be objectively? I suck at layout, they're one of the reasons I've put some mapping projects on indefinite hold, so definitely don't ask me
!