Taking many suggestions from the boards I changed it thusly:
1. Corrected the dwarf guards/cult guards typos, etc., up top surrounding the mine.
2. Forced the players (unbeknownst the them) into the Bhaal caverns first where they enjoyed the underground setting. They killed Grallak and got his mad writings.
3. Upon return to the black cathedral I had the elevator lowered and foot prints clueing the party into the fact that Dourstone had probably sent down Covenant Dwarves after them. The clues lead the PCs to the Myrkul maze.
4. Truncated the Myrkul maze a great deal and put in the Dwarves from the Covenant, who, like Dourstone, are beguiled by the Faceless One to try and help him keep the invaders out (Faceless One started the whole Dourstone involvement so this seemed to make sense). PCs captured Faceless One, took his cipher, and then went back to the Black Cathedral.
5. Tried the whole Theldrick: "It's illegal for you to come in here!" thing but the PCs basically called bullshi* on that because they are the types to stamp out members of evil religions on sight. They invaded and Theldrick, having had plenty of time to know they're coming, has set up a strong defense with all of his available resources.
6. PCs fought their way through to Theldrick who escaped them while his minions delayed them. PCs, knowing they had missed someone important, chased him out to the black cathedral.
7. Ever since they had killed Grallak, and then intensifying after Faceless one was captured, I had tremors shake through the area. Now, the PCs reach the Black Cathedral just in time to see Theldrick calling for the Ebon Aspect to rise. Rise it does, grabbing Theldrick and "absorbing him", much to his surprise, and then attacking the PCs who use every last spell to defeat it.
8. Finally, the red ruby they took out of the forehead of the statue in Theldrick's main hall begins to pulse once the Ebon Aspect is dead... my thought is that this ruby is some sacred relic of the nearest Bane church. Theldrick stole it before coming down into the mines and the Ebon Triad's process of raising the Aspect has kept its dweomer supressed. But now that the Aspect is reduced in power and this pocket of the Ebon Triad has been vanquished, the ruby will alert nearby Baneites as to its presence... this will allow me to have a higher level Bane cleric track the PCs down. Realizing they are actually helping his church by killing the Triad's splinter-sect members of his Bane Church... he will begin helping the PCs. Will they stand to have the Black Hand aiding them in their holy quest? A good moral dilemma.