So, now with 12V applied I get the proper 3.3V at the point on the board marked "3.3V" and at pin 1 of the ATMEGA328. I connected the FTDI and verified I could upload a sketch to the 328 by uploading the Blink sketch from the Arduino examples. I tested it by measuring the voltage at pin 19 - it alternated between zero and 3.3V as expected. Definitely making progress! But still some issues with RN52 programming. I'm going to post on the "How to: RN52 programming and configuration" because the issues are similar to others on that thread.
NC, USA; 1999 9-3 S, AS2; BlueSaab v3.2, software 4.1