I have been contemplating both the Air National Guard or the Air Force Reserve.

AH! But the question is........are they contemplating YOU!
1. Is it really difficult to get a pilot slot in either one?
yes - all military flight slots are very competitive - but you'll never know if you are until you try. (Just have a few backup plans)
2. How does one go about applying?
NUMEROUS threads on this subject, pus check out baseops.net' forums for more in-depth inforamtion (hint - - read MUCH MORE before posting over there)
3. If I had a medical disqualification from enlisting in the Navy years back, do they have the same standards?

YIKES!
You had a medically disqualifying condition for enlisting in the US Navy? If so - - military flight physical are QUITE A BIT more stringent. Unless it is something that has disappeared over time or gotten a lot better that is not good and does not bode well....but again - try and have them tell you NO.