2 initial reactions:
1) X99 series is not "officially" supported under OS X by Apple, so anything you do with a CustoMac build is all experimental at this this stage in the game. So you may need to consider that some of your issues may be as a result of a non-supported motherboard/chipset/cpu combination.
2) Are you connecting your Focusrite to a USB 2.0 port & not a USB 3.0??
I totally understand if you don't have any ideas since X99 is experimental, but this build is running so smooth and stable except for the audio interface glitch it's hard to be soo close, but not finished.
Here's some more info, since I've play around with the kexts a bit.
[edit] don't know if this is significant but just realized I'm missing applehda.kext there is no file under s/l/e, should I snag one from another mac (mavericks or SL), or how do I fix this?[/edit]
Voodoo HDA 2.61 and Voodoo HDA 2.7.2 VT2021
seem to be the best option for my build and are so close to working. Logic's audio works for 30-40 minutes (huge improvement), stutters a bit, but a simple restarting of the app keeps me running - which I'm fine with (that's better than having to turn off speakers, unplug the interface and hope it works again). However, if I play songs on Spotify I only get ~15 minutes (slight improvement) worth maybe a little more.
Found out that streaming the music makes the issue worse (5 mintues) and playing off the HDD is better with Spotify offline yielding 10-20 minutes but then I have to unplug and replug in the interface for sound to work again.
Which USB port should work better?
If there are no solutions, would this be something I'd have to wait till the new Mac Pro is released, or do other x99'ers keep hacking in the meantime trying to find fixes like these. and I'll have to stumble upon it?
Lastly, is it worth trying the HDMI Audio sticky:
http://www.tonymacx86.com/hdmi-audio/143760-audio-hdmi-audio-applehda-guide.html or is that unrelated to audio interfaces.
Thanks again for you help BoomR, you've already helped a lot and I really appreciate it!