The 4060's are sensitive so they don't need a pre-amp as much as some other mics (including 4061's). It will definitely improve the sound if you use a pre-amp.
I don't think the R-09 can provide enough power for the 4060's to work their best. It will record a sound, it just won't be as nice as using a battery box.
So my vote is 4060 > BB > R-09 if you need small. 4060 > MMA6000 > R-09 if you want a better recording. I use 4060 > MMA6000 > JB3 and I have no trouble getting that into any venue. You can easily hide the MMA6000 and I just walk in with the JB3 in my bag and call it "My MP3 player."
I'm thinking about getting a R-09 or MTII, so I can have a smaller setup (the JB3 doesn't really fit in a pocket very well).