I've got the pair "adequately" working for now. A lot is debugged and working, especially for CW.
I'm using the "generic" wiring for Yaesu right out of the manual, which ought to work well (FlexRadio uses the Yaesu 8 pin microphone pinout). I have the microphone cables on order, so right now I'm working CW and RTTY. RTTY is done via software direct; CW via RemoteRig. Audio is from the regular rig output via RemoteRig.
Big problem is audio. Apparently, the default wiring for Yaesu as given in the manual gives you mono only, as I have verified (right channel only sent on both channels says my experiments).
But, the Flex 6300 and software actually delivers a true stereo (well, separable left and right channel anyway) that you can use in various interesting ways, such as one VFO in one ear and the other VFO in the other. Or just listen to both channels the same. But, it's making them "different" that interest me and so I want true "stereo" output. Or, it's equivalent; L on L and R on R.
I really need that feature for Navassa and other larger pileups. For run-of-the-mill operating, monorual is working fine. How do I wire it for generic microphone (which is fine with me -- basic Mic+ Mic- and PTT is all I need) and yet get stereo output so I can have the features that really help?