1. FSA Ganondorf was a Geurdo while the Gerudos were not even present in AlttP, however for all reasons we can assume that he was one too.
The notion of the Gerudo hadn't been thought out by the time of ALttP, so we can't expect them to be present in ALttP; however, this does not mean that they do not exist elsewhere in the world of Hyrule. It is apparent that FSA takes place sometime before ALttP, even if it is not the Seal War itself. We see Ganondorf and Gerudo in FSA, which is not too far away from ALttP in the grand scheme of things. We could also assume that the band of thieves that accompanied Ganondorf were Gerudo, but that isn't necessary, because the Gerudo had little interest in the Golden Power outside of Ganondorf, as far as we know. Even if they are a band of thieves, we see them in FSA as a nomadic tribe, not reliant on thievery in the slightest, so we can assume that the Gerudo have changed significantly since the days of OoT.
Blue Window said:
2. If I remember correctly there is no mentioning of the Dark World turning Ganondorf into Ganon in GBA AlttP.
This is stated both explicitly by many NPCs, in addition to being mentioned indirectly. It is clear that what transforms Ganondorf into Ganon is the power of the Dark World. The whole bit with the Trident of Power just bungled a perfectly reasonable explanation Nintendo had going for a long time, creating ambiguity and inconsistencies everywhere. Unfortunately, inconsistency is the story of FSA; this has led some to regard it as non-canon, but just because something doesn't fit well isn't enough of an excuse to pretend it doesn't exist.
Here are some quotes from GBA AlttP that suggest that it is the Dark World that transforms Ganondorf:
Ball-shaped Man in the Dark World said:
And everyone who wanders into
this land is changed to a shape
that reflects his true nature.
I'm always changing my mind,
so I turned into a ball...
But if you have a ball called
the Moon Pearl, you can keep
your original shape here.
Sahasrahla said:
Link, it is I, Sahasrahla the
elder. An orb known as the
Moon Pearl rests in this tower.
He who holds the Moon Pearl
is protected, and his form will
not change in the Dark World.
You must find it and escape
from the tower!
Do not forget the Moon Pearl...
Maiden said:
You are the only
one who can destroy
Ganondorf, the thief... No!
Ganon, the evil King of
Darkness!
This quote establishes that Ganon and Ganondorf are the same individual, and the maiden corrects herself by saying that Ganondorf the thief is now referred to as Ganon, the evil King of Darkness.
Tree Transformed by the Dark World said:
The man who last claimed the
Power of Gold wished for this
world. It reflects his heart.
Yes, I came here out of greed
for the Golden Power, and
look what happened to me...
To restore the Golden Land, a
person worthy of the Golden
Power must defeat the man who
created this place...
Until that time, I am stuck in
this bizarre shape.
But what a mischievous thing
to leave lying around...
The Power of Gold...
Triforce...
With some extrapolation, it is pretty clear that the tree is referring to Ganondorf, and that people who enter the Dark World are transformed by its power.
In response to the original poster, FSA was a very confusing game in terms of inconsistencies; in general, it caused more confusion than issues it resolved. Much of this arose from the disagreement in the development team, as the game was initially planned to explain the Seal War, but was then changed to something entirely different. Unfortunately, many of the elements that shared similarities to the Seal War were left in, and this created a game with implications that should have not been there in the final product. The end result is confusing, but the placement that makes the most sense for FSA is still before ALttP. Calling it a proper prequel would be an unfair statement, but it is probably a game that comes before ALttP.