First - I figured out the discrepancy between my manual calculation and the program I was using! It was actually kind of a silly thing, but for some reason it didn't occur to me. That makes me feel more confident in the analysis procedure.
Second - I'm 2/3's done my last analysis step! That's right...in one day I went through 66.66666666% of it. I will hopefully be able to finish up the last 1/3 tomorrow (in between meetings and such). That still gives me 2.5 weeks to play around with other analysis techniques if I so choose (but will talk about this with my supervisor tomorrow).
The best part is the results I'm getting aren't nearly as bad as I thought they were going to be! They're not stellar, but they're better than some from a previous, similar, study --- always good.