I ran this under 3.0 rules and, like much of the City of the Spider Queen, it was tough. I allowed my players to min-max more than normal since the modual was a break from our regular campaign and I realized that it would be really tough otherwise.
If a character has access to a spell like Ghostform (from Tome and Blood) or can go ethereal, things are a little better but a frontal assault is suicide. A lot of this boils down to "every round you have at least a 5% chance of death" which isn't cool for players.
One of the things I did to make the paperwork easier for me was photocopy the map and keep track of who was where (you could blow up the copy and use little tokens to mark certain NPCs for just keep a running tally in the margin). In enclosed spaces with a set number of named NPCs this helps the DM to coordinate tactics.