To me the events of SS are easier to get if you adopt the perspective of a third observer, which doesn't travel in time at all but sees all the events from the beggining to the end, basically it would go like this:
1) SS Intro
2) Goddess sword created, skyloft sent skyward
3) Demise imprisoned in the sealed grounds
4) Impa leaves through the gate of time
5) Hylia and Impa arrive from the future and go to the temple of Hylia
6) Some hero appears out of nowhere, speaks with hylia, and leaves with the true master sword, leaving a sleeping goddess behind
7) Random fabulous demon comes from the gate of time, with the goddess' body and starts reviving Demise
8) Hero comes with a kickass sword and slays Demise, imprisoning him in the master sword
9) Hero leaves the sword there, note that there are two swords now, a goddess sword in Skyloft and a master sword in the temple of Hylia
10) Hero disappears, leaving with the goddess Hylia and leaving a sleeping Hylia behind
11) Centuries later, Hero is born
12) starting events of SS
13) Impa and Hylia flee through the door of time in Lanayru's temple of time
14) Forging of the MS
15) Hero enters gate of time, returns with the true MS [from Link's perspective, he went to (6) and returned]
16) Hero gets the triforce, and kills demise forever
17) Hylia awakes and is abducted by Ghirahim into the portal, hero follows them [From Zelda's, Link's, and Ghirahim's perspective, they skipped to (7), (8) and (9) and then returned]
18) hero and Hylia return, hero is swordless
19) Hero sees the master sword, other events of the ending take place
Some parts, particularly (10), may seem weird, but it all makes sense.
Noteworthy:
From (8) on, there is always a master sword in the world
and from (13) until (16), there are two master swords present
before (13), we had the goddess sword, created in (2)
If the master sword sealed demise in (8), then he was sealed into it until (15), by that logic, the sealing spike is the master sword
Proof that Link doesn't kill Demise in (8), but rather seals him, is that f he died, Zelda would have awakened immediately, instead she awakens in (16), when the triforce kills Demise
From link' (and therefore the player's) perspective, first goes (11), (12), (13), (14), then (15), (6), then (15) again, then goes (16) and (17), then goes (8) and (9), finnaly (18) and (19)
From Zelda perspective, it's (12), (13), (6), (17), (7), (8), (9), (18) and (19)
Impa's perspective is a bit tricky, it's (4), (12), (13), (5), (6), (7), (8), (9), (10), Impa gives the bracelet in (10), and then waits centuries in the temple until (11) and the rest of the events unfold linearly for her
Ghirahim's perspective, it's from (1) all the way until (17) (of course assuming he was during the events of the intro, maybe he wasn't born until later), he goes to (7), (8), and dies (presumably)
Again, it's difficult to get but it all makes sense, it's the best way I could explain it, perhaps Locke could provide a better way to say it