Trey,
I was thinking about how best to keep track of students' scores (even just keeping track of a single student's scores!) and decided to put together a simple spreadsheet, with a tab for each student. I use OpenOffice Calc for spreadsheets, but you could do this in Excel if you use MS Office software.
Across the top of each grid, I have listed each component (Note Duration, Guess Key, Bass Staff Puzzle, etc...) and along the left-hand side I will indicate the date. So, like this:
Fruit Lines | Guess Key | Note Alphabet
Oct 1 (time/score)| (time/score) | (time/score)
Oct 2 (time/score)| (time/score) | (time/score)
It does mean keeping this spreadsheet open or easy to get to, and updating it frequently, but then you will have all the data in one place.
I hope this helps!

I can attach a sample spreadsheet if you'd like.
~Adrienne in Lexington, Kentucky, USA
Here is a picture of my spreadsheet: