I am looking at starting in on the Temple guild series of quests and I have immediately hit into the same issue I tried to skip over for the Cult. Namely, how do you trigger multiple objectives without using stages?
What I mean is that if Koal Cave shrine is stage 30 and Ghostgate shrine is stage 50, what do I do when the player goes straight to Ghostgate and skips over Koal Cave? Once you set a stage value, you can't go back and lower it.
Another issue to this is tracking individuals who are attached to a quest. For the cult, you have a quest to collect 5 bottles of brandy. You can talk to each of the Balmora innkeepers and maybe get 1 bottle each. But how do you track who did and who didn't give you a bottle? There are stages in TES3 for each one but in TES5, you can't do it the same way, since you can't lower a stage number. Are there local variables that I can set on a person that I am not seeing in the game? Something to say "if this person gives the player something, check this box or set this flag" so the NPC never does it again.
The immediate answer is to make small quests for each person. Ugh. Anyone have a better solution or can think of something in Skyrim that I can copy from? I can't think of a quest like this. Thanks.

I think if you setStage() to
I think if you setStage() to a lower stageNumber maybe the journal doesn't get updated, but maybe internally the stage is marked. So you could use getStageDone() instead of getStage() in your conditions ?
Since the NPC are unique, you can add a conditional script on them, add a conditional property to note that you have already interacted with them and then use GetScriptVariable in your conditions...
does that help ?