Okay, so basically I've made my mod, but there are still a few persistent problems with it. The most crucial one (the one preventing me from releasing) is that the few stage of my quest that have quest markers don't have them appear. What I did is make an alias for an object nearby where I want the player to go (usually an X marker) and set that as the Target Ref for the appropriate stage. However, these don't seem to be showing up, which is troubling. Is there something more I need to be doing?

Better yet, can someone give me a step by step for setting Quest Objectives that will make my markers work?

You must write SetObjectiveDisplayed(Stage) in the script, but your script must be write in the stages
also SetObjectiveCompleted(Stage) - for completion targets

Yeah, thats what I did.

Doesn't work?

Nope. I think it may be a problem with my save. If I posted a link to my Mod as is would you download it and take a look?

By the way you are right). I remember as because of the saved game, target didn't displayed

I've now tried this with another save. The markers still wont show up.

If someone wouldn't mind taking a look, here is my quest. The link is within the linked topic.
The dialogue is in the Quest titled TBJ01
the other quest markers are given by the books TBJVisarolsJrnl (located in the bed chest in TBJVisarolHeadquarters ) and TBJNotes5 (located in TBJThalmorSecretHeadquarters on the bedstand in the upper floor)
http://www.gamesas.com/topic/1354850-please-beta-my-mod/