Wow man, that's quite an undertaking!

My first thought was for a hex map layout just because of the various directions you can go but if you want to make this look like a regular map like you seem to be, then I'm thinking you need to just draw the whole thing out before you slice it up. Of course, then you have to go through and make sure all the text descriptions are exactly right. If the text was done first, which I'm guessing is the case, I think you are at the mercy of someone else's imagination. Hopefully, they don't have any mistakes. Pathways leading back unto themselves is another issue. Basically that doesn't exist in the real world unless it's a roundabout. If it's a physical impossibility (read magical cause) I think you are going to be a little stuffed trying to map it.

IMO, it takes a lot of forethought to draw out these 3/4 view maps because of overlaying elements. I think most of us just make the space by NOT piling things over the top of others. I had a little of that going on with my lite challenge this month. Most noticeable in the landing and stairs going up to the Creature room area just outside of the Laboratory.

What you have going so far looks great though, keep up the good work.