We've completed our first quest and I have a question about the Brothers Durnog quest. The quest book states that the two master giants (Munkar and Nakir) each begin with a speed of 2, armor of 6, and 5 EXTRA wounds each. Does this mean that (when playing a 3 player game) they each have the 10 wounds from their stat card PLUS and extra 5, equaling 15 wounds? Or does this mean that you ignore the stat card and each has only 5 wounds?

The quest book also states that they have stoneheart. Do they also have the abilities listed on the stat card for a master giant? Does this mean that they have reach, stun, sweep, and stoneheart?

Yes, 5 extra wounds means 5 wounds in addition to their normal wounds. They phrase it as a bonus instead of just saying "15 wounds" because giants have different normal wounds depending upon the game size (not different enough to be balanced, but that's another issue).

Yes, they have all the regular master giant abilities in addition to Stoneheart (though if the heroes are smart, the giants will probably never get close enough to them for it to matter). When a named monster lacks an ability that the base monster would normally have, that is noted explicitly in the text.