ANA (actually JAL also) has two reservation data base, domestic and international. If you purchase wholly domestic flights in Japan (in this case using Japanese website) then the confirmation number is four digit, not six digit as you have discovered.

However, four digit confirmation number is different from five digit PNR (yes, it is five digit, not six digit) used for domestic reservation. Confused? Four digit confirmation number is what usually used for reservation purpose with passengers. Five digit PNR seems to be used for internal purpose only, but show up on a small print on a boarding pass.

Anyway, if you have a confirmation number then you should able to go back to ANA’s Japanese website under domestic section and look up your flight details. You need date of the flight, flight number, confirmation number and your name.

As UA 1K you should get two free baggage with each weighing up to 70 lbs. (32 kg) for free for a flight to NRT. You bought separate ticket for NRT-NGO Premium class, which with your status 60 kg total of checked baggage allowance.

Since you have to retrieve your checked baggage at NRT to clear customs and re-check your baggage for your domestic flight, I think whether if UA agent in the U.S. can through check your baggage to NGO or not may make not much of the difference.