CJL

Will need a copy of your tune and a log of it happening.

Attach you latest tune after the firmware update and I will fix some of the idle stuff.  It looks like the tune needs a lot of work though.

I'd start with fixing your knock. 
Seems like its pulling timing left and right. (even when you just rev it)
Your DBW is in setup mode.. so not sure if you aware of that.
Your IAT might be interfering as its adding fuel pretty much all the time.
Raise your Overrun De-activation RPM in the range of oprating temp.. from 1500 say to 1800 see if that help with the dips.
Last but not least.. I'd enable Idle ignition. That should help with rpms dropping as well. 
 
Hope this helps.