I've had a bit of trouble with matching levels as well, even looking at the waveform in the DAW, the re-amped signal is visually and audibly different than the original, even when using the same profile.
I've been able to get it much closer messing with clean/reamp sens, but it's not just right yet.
I'm chalking it up to user error, maybe something in my DAW routing software or something.
I pick this stuff up slowly, it took me a bit to figure out why the "git analog" wasn't working very well for me. 
Thanks for the explanation Nicky, some of this comes easy, and some is like pulling teeth. I'm sure I'll get it.
Reading your post it just clicked with me why clean sens has no effect on git-analog...that drove me nuts one day trying to figure out why the knob wasn't doing anything...'doh!
Chris: by "unity gain", you mean 0db on the DAW slider, correct? What do level do you track at?
Monkey_Man , regarding the level readouts that we'd like to see, it seems like I have seen people recommend inserting a VU meter both at the very beginning and the very end of the signal chain of the DAW? Mostly for the purpose of making sure that a particular plug-in sounds better, and is not just louder. Might that help here, or am I barking up the wrong tree?