fjz
The MixControl 1.8 version was what I installed when I got my interface.  The 2nd Gen was not out yet, and I never installed any other software for my sound card since that first and only install.  I believe 1.8 is the version for the MixControl sofware, but the actual driver version it installed was 2.5.1 (at least it was for me at the time).

 
Then you are probably fine.  Focusrite has always been a bit vague on all the various versions numbers to parts of the system.  Between the firmware in the hardware itself, the audio drivers themselves(more than one of these since ASIO and WDM are separate) and the MixControl software there are a lot of different pieces of software each with their own version numbers.
 
As for the USB settings, the Win7 Device Manager has a view (View->Devices By Connection) that might help you figure out what is currently hooked up and how.  Every device will have a property page, depending on the device driver it may have options to control power and bandwidth settings.  You might be able to improve things there.
 
You might find that some of your USB ports are faster than others (depending on how the motherboard chipset is setup).  You should also try disabling the USB Media card reader (if it's plugged in) and strip down all the USB devices and hubs to just the minimum.  Might try making sure the Focusrite is on its own USB port/hub and not sharing with anything (follow how it's connected to the computer in the devices by connection view). 
 
Sadly what exactly needs to be tweaked can vary a lot.  I know for example I get much better performance if I disable the nVidia HDMI audio device which comes with my video card (and gets re-enabled every time I update the video drivers).
 
You might also want to try harder to get that USB hotfix to apply (and also apply any and all Windows updates that are available).  Though that may just be a wild goose chase.

SGodfrey
I'm not really an expert but I did have some dropouts, clicks and pops recently and found the most comprehensive and easy-to-understand guide to solving it was here:-
 
https://support.native-instruments.com/hc/en-us/articles/209571729-Windows-Tuning-Tips-for-Audio-Processing
 
In particular, check out section 4.5.2 "USB Power Ports Power Settings", I don't think anyone has suggested that yet.  Also, are you using all the features of LatencyMon to try to track down the driver/process causing the issue? this is also covered in the above guide.

Yep.. the usb power settings are indeed one of the tweaks I've done already. 
 
That link looks like a great resource, so I'll be reading through that one for sure.  Thanks for posting it.

msorrels
 
You might also want to try harder to get that USB hotfix to apply (and also apply any and all Windows updates that are available).  Though that may just be a wild goose chase.

msorrels... this "wild goose chase" might prove fruitful after all.  I have a habit of not installing the optional Windows updates.  I had 70 of them waiting for me.  After installing them all (with many reboots in the process), it looks like my usb drivers have been updated.  The version number is only slightly different (after the third decimal point), but different none the less... So that's good news, I think.
 
I'm still having some issues, but this time it looks like ataport.sys is the main culprit.  My next step now, I guess, is to look at updating the drivers for my SATA controllers.
 
Thanks again for all help.  Hopefully I'm one step closer to resolving these issues.  Finger are crossed.