Is the price of the Apple Care (student price) in any way negotiable?
No, if the student price is available only from Apple. If you check around the internet, you'll find AppleCare available from various vendors at prices less than list.
I bought an AppleCare kit for my Powebook($350 list) for $224 from a seller on eBay. Had no problems receiving it from the seller or activating it, but you have to be really careful making any purchases off of eBay. If the seller has a really good history of positive customer feedback, such as 97 -100% positive, then it's generally ok.
Does the warranty cover just about anything?
Yeah, pretty much, except for damage that you cause as a result of dropping your MacBook or dropping something onto it or spilling liquids onto/into it.
could I ask for a replacment notebook when (if) they fix these issues? Or would they not accept that as a valid "problem"?
Who knows, all you have to do is ask. Sometimes, by being persistent, a negative response from them is turned into a positive one.
As far as I'm concerned, Applecare is a "must have" for a laptop, since there's more chance of problems with a laptop than there is with a desktop unit.