Croesus
Adventurer
My goal here is not to rehash megadungeon design but discuss how to modify the theories to work with 4E adventure building models.
I understand you want to focus on 4E impacts to this method of play, but I can't resist making one suggestion that should greatly simplify your work - don't map out the dungeon.
By this I don't mean that you don't have encounter areas mapped out, as needed. I mean don't try to map out the entire Undermountain, 5' square by 5' square. Instead, use a flow chart to show how things connect. The flow chart is easier, less time-consuming, and much more flexible.
Take a 5-room dungeon and piece of paper.
Draw a circle - that's the entrance.
Draw a line from circle 1 to circle 2 - add whatever description you want to explain how the two connect (a well, a pit, a hallway, stairs, teleporter, genie grants a wish, etc).
Draw a line from circle 2 to circle 3.
Draw a line from circle 3 to 4.
Draw a line from circle 4 to 5.
Maybe you also want a line from 3 to 5 - if the party avoids the trick or setback, they can slip past the guards directly to the treasure, or rescue the princess while the guards are distracted.
The point is that it's extremely easy to add (or subtract) connections this way. You don't have redraw your intricate map, you simply redefine the connections between the individual areas. Just remember that connections show options the players have, once they've overcome the challenge - they're not encounters themselves. If a the hallway connecting two rooms is a trap, it's not a connection, it's a circle. In a way, you can think of connections as cut scenes.
I believe there's at least one good thread (from a couple years ago?) on using flow charts instead of maps - if anyone can find it, a link would be great.
Hope this helps. Good luck with your project.