Hi gregorybrown
You very probably have closed this matter since a long time. However, I like to comment as follows:
If I convert the .flac file to a .wav format using JRiver will the resulting .wav files be essentially the same as if I had ripped the .cda file from the Red Book CD in the first place?
YES, if the wma files are lossless (not only essentially, but equally)
Should I use the original .wma file, or the converted .wma to .flac files to generate .wav format files?
If the original wma file is indeed lossless, it doesn't matter, Basically, the same digital information on both formats.
BDW, I did a mass conversion from flac to wav a couple of days ago (to fill a USB stick with music). I am very impressed with the sound quality (USB stick into the Marantz SA8005 and from there to the integrated amp).
Best regards