A change in fortune
Anyhow, it was an educational process, not just because I had to learn it, but because I learned a little more about how I learn. In the past few months, I used always taking the easiest possible way to accomplish whatever routine tasks I needed to get done, which was always frustrating. I didn't know either component well enough, and I wasn't learning - I was just working on a "don't break anything basis".
This time, I started by reading the documentation, and looking for new ways to do it all, and came up with a pretty efficient and relatively elegant way of doing it. I learned more in trying things that didn't work, than I have in a while - and I accomplished my goal. Fast, efficient and correct code. (Yes, I did do the verification.... painstaking comparisons of DNA strands and mutations.)
So, while I can't get the work back that I did in the past 4 months, I at least now have a solid foundation to work from - I'm ready to start tackling some datasets!