Wonderful ideas Kalencia!
Using orb form Nue would be take alot away of the epicness factor, yes. Byakuren would indeed make a good Agahnim, looking at her connection with Nue. Then we have an actual magician to fight! And now Yukari can stay Vitreous.
And Mothula should be Mystia, yes. Mystia appears in the bamboo forest, and Mothula's dungeon lies in the forest. Her darkness song also fits the Mothula battle: during the Mothula battle your on a multitude of moving floors that throw you into spikes along the wall. Mystia's darkness song would then provide an extra hardcore aspect to the battle. The fire rod was effective against Mothula, and said rod could light up the darkness to temporarily reveal Mystia.
Ah, yes, Yuyuko as Zelda already counts as a maiden. Since Utsuho is such an destructive maniac, she wouldn't be a good maiden. We could remove her from the other maidens.
And it looks like I forgot I already made Remilia Blind. Though Flandre may indeed be a better blind, considering she pulls off the innocent girl and monster parts better than Remilia. And disguised Blind stsrts off as a caged girl. Flandre could do the same with her basement. Perhaps Flandre got manipulated by Nue to lock up her own sister (it could be justified in that Nue told Flandre that it is all a little game, and Flan loves games afterall).
I personally think Nue would make the better Ganon. If Nue is Ganon then I think Byakuren would fit better as Aghanim since she is a magician after all.
As for Mothula it would have to be a character who has wings. Like either Utsuho or Mystia would be good candidates. I'm really liking the idea of using Mystia though since if we go with her then the entire boss room could be dark like this:
Koakuma would probably be a good candidate for that bat that appears when you use magic powder on that green fountain in the cave near the dwarves? house.
As for the Loyal Sage Reimu or Sanae would work best for that role. Just have to replace the church with a shrine.
Ah yes, I couldn't figure out anyone yet for those roles, yet I oversaw the most obvious choices. Koakuma might actually try to be a rough, tough demon, only to fail spectaculary, and I think Reimu would be a good Loyal Sage, since she's more 'no nonsense' than Sanae, and actually knows Yuyuko.
But what would the Triforce be? Do we know an object in the Touhou games that has similliar powers? The series has many powerful weapons and items, but it lacks an almighty, wish granting force (not counting Yukari, since she's a living being, not an object).