There's a lot going on in this post, so...to help me keep it straight...numbers!
<1> The difference in FLAC file sizes, even after using level 8 when compressing via CD-Wave or FLAC FrontEnd is probably due to a version difference - CD-Wave uses one FLAC version, FrontEnd uses another. Don't sweat it right now.
<2> The static could be strictly a function of the playback decoding and it may not have anything to do with the encoding to FLAC. Without more testing, we can't know one way or the other.
<3> Sounds like FLAC FrontEnd is working just fine...not sure what the problem is?
<4> I thought you were starting with 24/48 files, so I'm not sure what you mean by "drop down the bit depth to 24 and the sample rate to 48000" in CD-Wave. Isn't that your starting bit depth and sample rate? At any rate, back when I used CD-Wave I would join my WAV files in my editor, do any processing I need, and then track in CD-Wave as the last step. So try joining the master WAV files in SF first, do your editing, and then track in CD-Wave. As an aside, if you'd like to figure out the error you're receiving, we'll need to know, at minimum <a> whether you selected the Alternate 24-bit Format when exporting from CD-Wave, and <b> what the SF error message says, exactly.