I found what I needed to finish the Drow city, but there were two doors left that said, "to pass is death...you need a wardstone". How many did you find and where?

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You are either trying to enter House Jaellat or the Tower of the Lich. In either case you need to find some guy selling a wardstone. He appears south of the Female Fighter Society after you kill some Ghaunadar Worshippers for a matron mother.

The thief (actually a mage) you mention sells a magic rope that allows access to the Lich Tower. In the Lich tower, you find the wardstone for House Jaellat. When I went to House Jaellat, the wardstone disappears after entering the first door. The 2 upper doors still say, "...to enter is death....you need a wardstone". Is there anything else to this?

On another note, there is a door similar to this in the gate district? It doesn't ask for a wardstone, but won't let you pass for some "weird" reason.

Don't think so. You get into House Jaellat no matter which door you use (there are only 2 doors anyway right?)