You'd think that Craig's salary etc for the trilogy would have been worked out when they signed the deal for the first one, wouldn't you?
Craig and his agents should be wary of reading too much into the success of Skyfall, IMHO. I think the real star of that movie was James Bond, not Daniel Craig. There is no doubt that Craig is an excellent Bond and that Eon should pay him huge sums of money to remain in the role. However, the fact remains that outside of 007, he is not really a massive box-office draw. The Golden Compass, The Invasion (the Body Snatchers remake, Cowboys and Aliens, even Dragon Tattoo - underperfomers all.
I' not convinced that his presence will benefit the sequel all that much and he could just end up pricing himself out of roles at this rate.