sock monkey
" as I sang some test passages, and everything stayed in the green, no yellow/red. But when I would play back. louder passages would have a sort of clipped sound, almost as if someone had applied a way too-heavy brick wall compression on it."
 
Here seems to be telling the story... If the Scarlett and Sonar do not show clipping yet you GET clipping, this points at something wrong with the mike. 
 
 

Or the cable... which is where most of my noise problems tend to come from.

I've made vocal recordings via my Focusrite interface that were clipped, even though the levels were OK within SONAR and I didn't notice any clip indicators while I was recording. It wasn't until I began mixing that I noticed harshness and saw some flat-topped peaks. I suspect there isn't as much headroom in these mic preamps as what I'm used to, making it possible to clip without noticing it's happening.

bitflipper
I've made vocal recordings via my Focusrite interface that were clipped, even though the levels were OK within SONAR and I didn't notice any clip indicators while I was recording. It wasn't until I began mixing that I noticed harshness and saw some flat-topped peaks. I suspect there isn't as much headroom in these mic preamps as what I'm used to, making it possible to clip without noticing it's happening.

I had a LOT of clipping problems/wildly fluctuating levels using the Inst. input on the Scarlett while recording bass. Partially due to poor technique and pickup that sticks up too high at the low E string (one of the plastic mounts is broken because some dumbass dropped it while skateboarding with it sans case... grrr). Once I started putting the bass through my amp head it evened things out. I'm getting a better tone this way anyway.
 
I had similar issues with my guitar tracks. It's a nice input and sounds pretty good for a multi in but it ain't perfect... that's for sure. Still much better than the multi ins on my Layla from what I can hear.

I noticed the same "low level" headphone output issue with my Focusrite. Since I have 8 outputs I simply ran one pair to the AUX in on my stereo system receiver and the headphone levels were no longer a problem.
 
I have since picked up a Behringer 4 ch headphone amp so that I can easily use multiple headphones for singers and others in the studio. 
 
Those are my solutions and they both worked wonderfully.

sock monkey
" as I sang some test passages, and everything stayed in the green, no yellow/red. But when I would play back. louder passages would have a sort of clipped sound, almost as if someone had applied a way too-heavy brick wall compression on it."
 
Here seems to be telling the story... If the Scarlett and Sonar do not show clipping yet you GET clipping, this points at something wrong with the mike. 

Or the input gain is turned up way too high in Sonar. I'm betting the OP is not taking this into account.
 
#28.

I know nothing about the interface you are using, but I can tell you that a number of years ago I got some new headphones that were AKG.  I have no idea what model they were, but they were a give or take $100 pair.  They sounded great and were "open", but they were nowhere near loud enough to monitor recording my drums.  I had been using some Sony phones that were "closed" and a LOT louder.  The primary difference was the impedance of the AKG phones was much lower than the Sony pair.  I ended up taking the AKG phones back and getting some replacement Sonys at the time.  Now I have some Bose phones that work well volume-wise, and sound good, though I think I may still prefer my old Sony phones if I still had them.  And I generally don't care for Sony stuff.
 
Hope this adds something.

Or the input gain is turned up way too high in Sonar. I'm betting the OP is not taking this into account.
 
Only you interface controls the level while recording. This is where they are having an issue, They are turning the gain way down too low because of random clipping. 
I'll also agree that the focusrite pre amps are not as forgiving as any others I have used in the past.. they are way to sensitive for my liking. 
 

MacFurse
OK. A lot of that now makes a lot more sense. My wife is an extremely loud singer, and mic technique is everything for her, and she is the reason I initially went down the pre-amp/comp on the input stage.

If your wife sings loud and wants to get close to the microphone, you may be better off with a different microphone. I don't see a traditional vocal mike in your signature, but if she likes to manage proximity actively (a lot of jazz singers are aggressive with this), then it might be better suited to a handheld dynamic with a high SPL tolerance. Even an SM58 does a great job on vocals; I often use a Sennheiser 421 on a stand for loud singers (and saxophones as well). Dynamics don't get enough love...

I like a 57 on female vocals sometimes!

Sanderxpander
I like a 57 on female vocals sometimes!

Have you ever used a Shure Beta 57? Awesome mic. It's got the nice crisp high/mids of the classic 57s and Beta Greens but it's built more ruggedly like a 58 so it isn't all sharp and prone to plosives/feedback/bumps/etc. It also handles low end better than a 57 without the dull mud of a 58.
 
I got to use one for a few years for some higher/mid freq vox that went back and forth from soft melodic to screecher. Very nice blend of the two mics and I soooooo want to buy one (but they are more expensive than the 57 or 58). 
I see now there is a Beta 58a (not sure if that's new or what). I wonder what that's like. I like Beta greens for vox but they lack balls. Regular 58s are just too damned muddy and boomy for my taste even if you can whip them against a concrete wall and not break it.