Getting everything indexed, which took 2 or 3 days (partly because I was doing pretty small chunks, partly because of the issue below) seems to have helped a lot.
One thing I ran into as I was doing it is that, 2 or 3 times while copying stuff over, it just stopped indexing anything. I tried deleting the 5 or so that were on there each time it happened, but it wouldn't index anything else either. I deleted a few things that were already indexed and it started working again. Not sure if it was just kind of hung-up and deleting something cleared that up, or if there is some limit on what it will index that is different than the index on the device. As long as it was taking I didn't really feel like experimenting
Anyway, I just wanted to let people know that it was a bit of a headache, but it did help, and thanks again for all the assistance.