Dropping in to update and drop in a few responses to the thoughts above.
First of all, thanks everybody for your thoughts. It's all really, really helpful. Toddbishop's advice to isolate the right foot was especially important - I actually got the same advice from my teacher that week. I just crank out sets of 2, then sets of 3, and then sets of 4 16th notes for about 10 minutes during each of my practice sessions. I work at as high a tempo as possible, both right and left feet. It's really making a big difference in my grooves and my ability to work the systems.
Right now I'm booking about 10 hours a week behind the kit practicing. It's all in the morning, when I'm in peak zone time, so I'm actually making progress a lot faster than I was expecting. I have chosen to work one system at a time. Once I get to the later pages of reading (IV and up) I start working simultaneously on the next system I find interesting, and split my time. This is because my right foot gets tired once I have to crank out sets of 3+ sixteenth notes! Working on two systems, I can alternate and give my foot a break.
I don't do any warming up other than singles with my hands/feet a few times a week - I just jump right into the system I'm working on. After about 20 minutes, things are really grooving and I'll stop and use the groove on whatever song is appropriate in my collection. So, I always jump right into USING the system with music as soon as it feels natural. Once I play a few songs, I'll jump back into the system and keep working the reading for maybe another 15-20 minutes. Then I'll either play more music or work on learning a fill. By that time it's time for me to leave and go to work.
With this strategy my playing has become the best it's ever been, and I can master a system well enough to really, really groove it with the music I'm playing. When I play music, I try to also work in the fills I'm practicing so that I can move them into the system without interruption of the left foot, etc. If I drop the groove, then I'll stop the music and work things out slowly.
The whole thing is working really, really well and I would definitely advocate this kind of routine for anybody with limited time.
-sheldon