I agree with Henrix on 2. and 3. However, with regards to 1., the description of the
negative energy protection spell states as follows:
The warded creature gains partial protection from undead creatures who use negative energy and certain weapons and spells that drain energy levels. The negative energy protection spell uses positive energy, which can offset the effects of a negative energy attack. Each time the warded creature is struck by a negative energy attack that drains levels or ability scores, it rolls 1d20 + caster level against a DC of 11 + the attacker’s HD.
There are therefore two questions presented here: a) is the dragon's attack a negative energy attack? and b) does the first sentence of the above description limit the second and third sentences?
a) If the dragon's attack is a level draining attack, my theory is that it HAS to be a negative energy attack, and therefore subject to the protection afforded by the
negative energy protection spell. Theoretically, however, your DM could invent a monster that drained levels using energy other than negative energy; if this were the case, then by the strict wording of the spell, NEP would not protect against the dragon's energy drain attack.
If the attack involves ability drain, then it also probably should be a negative energy attack, but there is a greater likelihood that the attack could be something else (there are both poisons and diseases in the rules that cause permanent ability DAMAGE, which has the same functional effect as ability drain). Once more, it depends on whether your DM categorizes the attack as negative energy or not.
b) If one adopts a mechanistic reading of the rules, then the first sentence of NEP can be held to apply only to attacks by UNDEAD creatures or by special weapons or spells. If the dragon in your example is not undead, then NEP would not apply. Personally, I think the spell text should be errata'd to remove the word "undead," but it's part of the rule for now. Thus, if your DM reads the rule strictly, then NEP would not apply to a dragon's attacks, even if they channeled negative energy, unless the dragon were undead or unless your DM considered the dragon's attacks "weapons. . . that drain energy levels."