I didn't notice any missing textures, although I did see many misaligned. Like id1 misaligned :) Still, it didn't deter me from the gameplay, which was enjoyable. The second map was the best of the three, showing off some nice detail and backtracking.
As others have said, its rough around the edges, but its far from the worse thing I've played. With a little more polish, I'd give it a solid thumbs up. Fine work :)
First run demo, hard skill: http://qrf.servequake.com/~orl/misc/orl_MJB2.rar