Some of these I'll answer.
Emiliano can answer others if he wants.
There's pieces of the story not fully revealed to the reader. You have to fill in the gaps, or invent your own, depending on how you look at it.

The crystal was trapped in another dimension originally.
But obviously Skeletor had a great section of it in his posession.
How did he get it? How long had he had it? I'd rather hear fan ideas/theories. In reality, we hadn't mapped out an
exact chronology of how this all occured, even though we had an idea.
You have to consider, Evil-Lyn is very much on-the-outside-looking-in on much of Skeletor's life, despite thinking she has more of a grasp on things.
Skeletor's no moron. He keeps his own eye on Evil-Lyn. There's not much that escapes him.
I explained the transporting in another thread a long time ago, I believe, but I can't find it at the moment if it's still here.
At that time, Skeletor relied on spells involving runes to transport from place to place (we were working on evolving the non-teleportation standard in the MYP cartoon).
Trap Jaw's power boost is connected to a Filmation episode. I'm sure someone else can explain that one.
What happened to the Unnamed one?
*shrugs*
The concept of Nordor was one of those "all the pieces of the puzzle were there" things. We talk a bit about it vaguely for a moment in episode 015 of Roast Gooble Dinner. It wasn't something previously laid out, but just came natural when viewing the existing story elements.