I do like @Caitlyn's suggestion.

But maybe could borrow from the job quests as well - i.e. monk to get the crystals would go do what they do 30-50 or so, bard looking for new songs(maybe need to trawl through the inn's and taverns) - that in the end create a crystal - etc... etc...
It would feel original at least even if in the end it would all be go to point A, click, go to point B, click etc...

Step 2 ok the dungeons are kinda ok...

Step 3... I'd use primals(or any other 8 man duties really) - all of them - get a mark list as such that lists 3 to do from all available through DF - do them get a drop - maybe mix it up so that you need to do multiple lists to complete one item.

Maybe some items would require same ones to be run to get a different drop - the mark list would define what drops., Adding a bit of poe and law into the mix would help out as well.