Now that I've finally got my head around the gain staging, I decided to re-record some guitar tracks. Plugged into my Focusrite and tried to get the appropriate level reading on my track meter. It was running too hot, so I turned down the gain knob on the Focusrite, then turned it down again, and again, until it wouldn't go any lower. Still getting a relatively strong signal into Sonar (fader at -10dB). So basically, I can't record a signal below -10dB.
 
If the gain knob on the box is at zero, why am I getting such a strong signal? If I turn it up high, it obviously clips, so I know the knob is working.
 
Is this an interface issue? Can't be my pickups, can it?

Known issue with 2i2 and some guitars: https://www.gearslutz.com/board/newbie-audio-engineering-production-question-zone/741268-help-focusrite-scarlett-clipping-problems.html
 

Maybe check the Line/Inst switch?

yes try the line instead of instrument. do you have active pick ups ?
if your on instrument and its still too loud, buy a cheap DI box w/ a pad switch on it.
http://www.guitarcenter.c...p;kwid=productads-adid

+1 to trying the line setting on the input. My pups are passive but run hot and I try not to attenuate at the guitar much, so line input on my interface gives the best range for input adjustment.

Depending on pickups and distance to strings you may have a stronger signal than most guitars (the interface needs to work for even guitars with weak outputs). Another option is to lower the pickup height slightly and see how it affects tone, but I would go the line in route first.