I have finished building out the temple's questline. Just going through it all now and finding that there is so much more still to do in parts of Morrowind. Several shrines have everyone fighting each other (which makes it easier for you). But all the treasure is flagged as stolen. I've found several important enemies to be flagged as disabled by default. I have an issue with that because the dialogs allow you to already defeat this enemy and still get credit for it for the quest (I know not all do this, but the Temple quest do).
I'll upload it all here by the weekend. I want run through a few more times and make some Objective tweaks.

Issues so far: Seven Graces
Issues so far:
Seven Graces -
PuzzleCanal script needs to be created, otherwise you have to TCL through the forcefield to the daedra.
Chest of Silver Longswords looks empty but that is because the sword has no name and no mesh assigned to it.
Compassion -
Bulfim,the orc, just repeats that "You shouldn't be here" and therefore you can't talk to her for healing.
Ghostgate, Tower of Dusk -
There are some strange breaks in the hallway meshes that have gaps between sections.
Disabled objects -
Bjadmund, Raxle Berne, and Delvan Andarys are all disabled on startup. But these quests allow you to kill them prior to the quest, so I changed them to be enabled. Other items I only enabled during the quest as they should be.
Hair Shirt -
Feril only has a sword in his corpse's inventory but the quest item is in his actor inventory.
Four Corners -
Had to move dialog topics out of DagonFel and into each quest. This fixed the problem of Tholer not giving the next phase. Other option could be to merge the four quests into one large quest.
Compassion, MinistryHeathen, and CuringTouch -
Dialogs with diseased person were all broken, dialogs either under the MDQ dialog block or tied to diseas topic. In either case, moving to quest fixed the dialog.
Other snag I can think of is when using a cure disease spell on people. I don't know enough about scripting to check for this. So those quests only track if you gave a potion to the person.