Shrukan, most theorists believe that the AOL backstory, that is, the prince locking the Princess in the Tower etc, happens long before AOL and hence AOL can still be last.
I also don't see "The Master Sword Sleeps Forever" as sufficient evidence to place it last.
The games that are normally placed after ALTTP do not feature the Master Sword.
And its Appearance in the Oracles Series is an Easter Egg.
As for the Timeline that re-merges to form a single timeline again, as Shrukan said, its scientifically impossible.
If you have two different timelines, there are bound to be differences. If we merge them, how exactly do you propose we balance these differences of events and histories?
TWW is clearly closer to OOT than you give it credit for...And FSA show a close inclination to being before ALTTP...
OOT is no longer the seal war...As it was originally intended to be..