Rob,
" I do realize that any switcher must be HDMI 1.3 or else you will lose the lossless audio stream."
That isn't correct. You only need 1.3 to pass the lossless audio streams in bitstream format. You won't be doing that as you will be decoding in the sources to LPCM and passing that through the switcher to the CLUX. LPCM can be passed on all versions of HDMI though not all equipment may actually support that.
"Can anyone please tell me if you need to run the Gefen HDMI detective out of the HDMI output from the clux 11sa mod to keep the multi channel audio stream going?"
You need an active sink (display) with the CLUX all the time.
The Gefen HDMI Detective is needed if you run into EDID issues with the CLUX. Only getting 2 channels of LPCM or no audio at all from your sources.
If you are planning on having to buy a HDMI switch and a Gefen HDMI Detective consider just going with the Octava instead. It doesn't need the sink, with the 'Static EDID' firmware won't have the EDID problems and has switching built in.
Shawn