how did beast get to hollow bastion?
By his own sheer force of will. Nomura has commented about this in interviews. It's happened a couple other times as well, but the other examples are escaping me.

why isn't rikku the hero when he is linked directly to terra in bbs, but sora isn't but barely linked to ventus?
Riku is able to take the keyblade from Sora in Kingdom Hearts because he was chosen by Terra. Sora is able to wield the keyblade because Ventus's heart is within Sora the same why Kairi is.

why is neverland in EVERY kingdom hearts game except 2?
Why shouldn't it be? It's the one world where none of the characters age by the very nature of Neverland. It's perfect.

why is agrabah changed so much in 1 and 2, same with halloween town?
As you point out, it's a game.

how does merlin live in radient garden but without it being completely destroyed he is in traverse town?
Merlin has already demonstrated an ability to travel between worlds. All the other characters native to Radiant Garden also fled to Traverse Town when it was overrun by the heartless. This is explained by Leon in Kingdom Hearts.

Why is Sora voiced by a girl?
Fair shot at HJO, I guess.

how and when is re:coded supposed to take place?
The precedent for a digital world is set in Kingdom Hearts 2 with DiZ's digital version of Twilight Town. Re: Coded takes place immediately after Kingdom Hearts 2 in a digital world based on a data version of Jiminy's journal.

How does Sora grow over a foot in a year?
I grew thirteen inches in eighteen months. Your point?

why is Roxas Ventus?
Sora is a vessel for Ventus's heart the same way it was a vessel for Kairi's. When Sora releases Kairi's heart with the incomplete keyblade made from the Princesses of Light, it also would have released Ven's heart. Ven's heart went with Sora's nobody--a shell without a heart--and essentially Roxas is created in Ventus's image. Xemnas's reports suggest that Roxas has a heart, and it is entirely likely that Roxas is literally Ventus reborn, hence the ability to use a keyblade.

How is it that terra goes to cinderellas castle after ventus, but is at the dwarf woods before ventus, when that is the first place Ventus goes????????????????
He left first and traveled faster? You're thinking about it too much.

Further, Kairi cannot create a heartless. When a person's heart is consumed by a heartless, it is the darkness in their heart that spawns a heartless. Since a Princess of Heart has a pure heart, there is no darkness in her heart to make a heartless.

Sora became a shadow heartless because he was a naturally created heartless. Other heartless were artificially created by Xehanort's research in Radiant Garden. Since Sora became a heartless by releasing his own heart, not by being consumed by a manufactured artificial heartless, he became a shadow.

As for why Sora was able to retain his memory, the Xemnas Reports mention that only Sora and Xehanort have been able to retain their identity as heartless. Sora and Xehanort have one important thing in common that may be the cause of this apparently uncommon phenomenon. Specifically, at the time they became heartless, each of their bodies currently possessed multiple (three, in both cases) hearts. Sora's body held his own heart, Kairi's heart, and Ventus's heart. Xehanort (or Terranort, I guess) held Terra's heart, Xehanort's heart, and Eraqus's heart. This is likely the reason their ability to retain their minds as heartless occurred. One might be able to argue that Sora's heartless was spawned of both his heart and mind while Roxas was formed of his body and Ventus's heart and mind. This, consequently, might suggest that Xehanort's heartless was made of Xehanort's heart and mind while Xemnas was formed of Terra's body, heart, and mind (while lacking memories). Or some similar combination of the above.

For how many holes Kingdom Hearts II left us, the additional titles really have done a remarkable job of giving them pretty consistent explanations. I don't like to give Nomura credit, and I certainly refuse to say that he had this all planned out from the beginning, but he has done a very good job of making a good continuity.