Once you're geared and know the fights start the hard modes. Some might be easier than others. Either way though, you'll want to have the basic fights down very solidly before you begin working on hard modes. Don't try to run before you can walk. You'll just fall flat on your face and become grumpy.
"I was wondering if there was any new recipes learned via research in alchemy or inscription added in 3.1? I had stopped doing the researches before hand, and forget if there was new stuff added to make the uses worthwhile."
Not for alchemy. For inscription, you'll want to try to get your hands on the Book of Glyph Mastery to learn a new recipe from patch 3.1. There's several new recipes, so you'll need to get multiple books.
"Is there any way to make a macro that will not use a glyph that you have?"
No, once you have a glyph in the only way to cancel its effect is to remove it.
"I know honor caps at 75,000, and marks from battlegrounds cap at 100, but is there a cap for Stone Keeper's Shards?"
Either the cap has never been found, or it's so high you'll never reach it. Very likely the cap rests on the same grounds as the gold cap – the upper limit of whatever sized integer the Stone Keeper's Shards variable is. My guess is it's 2,147,483,647. That number is the upper limit of a signed 32-bit integer as represented by a standard C compiler. If that is all Greek to you, I'll put it another way: it's big. (Before people decide to nerd rage all over me because of a computer fact, remember that the gold variable is a signed integer as well, and we've seen other signed integers in WoW besides that. There is no indication that the variable would be unsigned, and every indication it would be signed - even if a signed 32 bit integer doesn't make sense logically. Live long and prosper, geeks.)
"Imagine you're reading the story of World of Warcraft. What race & class would be the protagonist? It seems like it would naturally be human or orc since those leaders are quite clearly the main players in the storyline. Human Paladin? Orc Warrior?"
I've been re-reading all the Warcraft stories lately. It's pretty clear to me that there are two main actors, someway somehow connected to everything: Jaina Proudmoore and Thrall. In this regard I'll say that those two are the closest things we have to universal protagonists. And to answer your question specifically, Jaina would be a Human Mage, and Thrall would be an Orc Shaman / Warrior (argue away lore nerds... argue away.) A case could also be made for Rhonin the Ro-ho-ho-nin, but to that I just say "nahhhhhh."
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