He guys I'm sorry that it took so long for replying. I have read up on the discussion and made some of my comments. I shall make them in the chronological order of the story.
1 ) I think that Link is going back to the Gerudo King is pretty much given. I don't think additional nudging would be necessary. To the player he is still a benevolent character at that moment. Not to mention that the Gerudo King would have told Link to return because he would research the locations of the others.
2 ) I think at that time it is best that the Gerudo King would give the locations of all 3 remaining cogs to Link. One with the Zora, one with the Gorons and one with the Hylian Royal Family (which we know is not with the Royal Family, but the player doesn't) and the Gerudo King would be better to search for the last ones location, because he can move freely through the Castle.
3 ) Mentioning Maple at this point is probably not to relevant on the story's progress. Because the Gerudo King would not reveal his true identity yet. Or he might not care because he already knows and knows that Link can best Maple, the hero cannot enter the shrines himself and he believes Link to be under his control. The Gerudo King would just be scheming at this point and let the future unfold.
4 ) Link would meet the Gerudo King in the Castle and when he leaves he would be caught by guards who want to throw him in the dungeon. But they are interrupted by Zelda. She recognizes Link from earlier and asks him what his business was in the Castle. Link answers that he had a meeting with the Gerudo King, but doesn't get the chance to go into more detail. Zelda starts to mumble that the Gerudo King has been spending a lot of time in the Castle's Royal Library lately. She then orders the guards to escort Link out of the Castle instead of to the dungeon. Once Link is outside the Castle he cannot get back in due to increased security.
5 ) The Deku Merchant would be standing in Castle Town next to a Gate visibly crying. You could even have a guard or a character like Eugene taking his statement and maybe one of the gangmembers trying to comfort him. They do not need to block the entrance or something as this gathering would probably be plenty of visible. The Zola who robbed the merchant are still on Hyrule Field on the path towards River Valley assessing the loot.
6 ) My initial thought for the fort was to give the player the option for sneaking or just battling his way in. But I do like the idea of several camps before the fort as well. We could even rate the player on how he goes through the fort (sneaking or battling) and have the reactions of the prince and princess depend on it. Having the princess preffer using her mind and thus sneaking and the prince preffer to use brawn and thus battling.
7 ) Collecting the materials isn't necessary and can be scrapped. I had the idea for lengthening the story because this part seemed short compared to the Hyrule Town/Deku/Kokiri part towards the first dungeon. But hey scrapping it is just fine with me, when you put small puzzles in place to the ancient devices.
8 ) I think that Link should battle Maple at the first device and the battle would damage the device [The why I will tell later]. You then get Sheldon and he will work to repair it. In the mean time Link goes looking for the other devices and turn them on. Once Link emerges from the 3rd device on to Lake Hylia again. A rumbling starts, because Sheldon turned on the first device again. Link will see the entrance rise from the center of Lake Hylia.
On the shore you will see the ancient Hero and Maple. Maple tells the hero something like "I was right in letting that idiot do the hard work for us. Wasn't I?" (As if that would rectify her earlier mistake) And Maple would then quickly rush into the Temple before Link. The hero would then disappear and reappear before Link. He warns/threatens Link that Link's life and every life in Hyrule would come to a horrible end if he continues on his path. And the hero would then leave again.
Link continues into the dungeon. He finds Maple knocked out by the Mini-boss. Link defeats the boss and gets the Cog.
Once Link emerges and gets back to shore he is attacked by a group of Zola wanting revenge for their fallen leader. But he fends them of.
Now for the whys of that last bit:
- Maple's fight should be at the first device, because it would allow some time to pass for Maple and the Hero to regroup before entering the dungeon. And let the Hero enter the story again.
- Having the first device be damaged allows Sheldon for some story time, but it also gives a delay in that Link can return to the Lake Hylia area and see the entrance rise himself, see Maple go in and be confronted by the Hero.
- Finding Maple knocked out in the dungeon indicates that Link has caught up and went pass Maple in the race for the cog (in the 3rd dungeon Maple and Link could fight together to defeat the boss).
- Facing the gang of Zola after the dungeon gives an epilogue to the Zora arc, just as the Deku Merchant gives a epilogue to the Deku arc. And enough time should have passed for the Zola to regroup.