Definitely, start with the waiver asap. About the 40J, I dont have clear answer either. I contacted the KCC and they said: "KCC is not authorized to assist you with this issue. Please contact the American Embassy/Consulate with jurisdiction over your area for further information". I contacted the US embassy and they said: "for that question contact the KCC, we only receive the application when its approved by the KCC". So, try both the KCC and the US embassy, maybe you are luckier than me and can get a straight answer.
On a personal note, I don't think that answer yes to the 40J will hurt you right now, given that all those questions (40) must be signed at the embassy when you have the interview. However I don't know the true answer, this is just a guess.