Whenever I run up to someone doing the same quest as me I try to hold back and wait for them to finish or help them fight the enemies in the area to speed up the process. It's just a little common courtesy and one always has to remember what goes around comes around.
I believe he is just talking about the red text that pops up when you try to use an ability that isn't ready.
As far as I know I don't think it can be disabled.
Right clicking is typically your basic attack, which should be the first option in your action bar. What you are seeing happen on your action bar is the global cooldown for all attacks. This isn't a pure action game so there is a bit of wait time between attacks.
http://www.giantbomb.com/star-wars-the-old-republic/61-24205/playing-the-old-republic-with-a-ps3-controller-walkthrough/35-528929/?page=1#div_shout_post_5060896
Someone did a nice little walkthrough on how to set it up.
Works well enough. You don't have the complete control you would have using a keyboard and mouse but for us console gamers trying to play the game this really helps you get into it. Obviously you will be at a disadvantage if you play PvP or if you group up with randoms who take games too seriously. But it's good for soloing.
Also consider that Razer keypad someone mentioned earlier.
Its in the options menu in the game. Should be a tab for key bindings. I pretty much use a keyboard for everything except for looting and interacting with objects, mainly because i haven't found a way to map it to the keyboard.
Knight gets a blue lightsaber, consular a green. You should have access to green, blue, and red crystals shorty after that. There are other colors as well but they are rare finds.
Not all items can be modded. When you hover over an item in your inventory it will tell you if you can mod it. If it can be modded just hold CTRL and right click the item.