Here's what I suggest.
1) Add more external campaign elements to the module. In my campaign, the clerics hired some re-occurring villains to ambush the PCs when they came back to the mines the second time. And, in fact, they had both the villains and some of their own clergy ambush the PCs, so that the PCs were left wondering whether the villains were always allied to the clergy or whether it is something else.
2) Have the Clerics actually do something other than sit around waiting for the PCs. In my campaign, each elemental temple was busy preparing to cast rituals at various times of the year. So, the Air Elemental temple was casting a ritual which would put a large hurricane level funnel of air around the entire mountain, making it nearly impossible for anyone to approach without magic. The rituals were scheduled for the Summer and Winter Solstices and Spring and Autumn Equinoxes respectively. This put a 3 month time table for the PCs to come in and stop each ritual (although the PCs were not aware of all of the rituals, just the "next one").
3) Have the PCs go off on other adventures sometimes. The Temple makes a great "Now that we are stronger, let's go take out the temple" type of adventure where the PCs can waltz through part of it until they find yet another "too tough to handle" situation which they can come back later when prepared.
The best thing to do is to make the Temple dynamic. As the PCs get further and further into it, have the Doomdreamers force the various temples to work together against this common foe.
One other thing I did in my campaign was to remove some of the cannon fodder. The orcs attacked the group, but when they were getting wiped out, the remaining orcs circled around the PCs and left the mountain the way the PCs came in. It does not make sense that all creatures would fight to the death. I had some of the wimpier creatures hide when they saw the PCs kicking butt on some of the tougher ones.
Good luck with your game.
