Not sure if rsync is the best backup solution, but so far it works fine for me. I have a copy of a known working image on my N900 which I update if something mayor has changed in my ED working image and I have a 2nd image ion my laptop.

I neither use r-base nor inkscape, but I have gnumeric installed and it works fine.
I run PR 1.3 and ED (v3e) from the first day and power kernel from extras (stable) repository (v42?) from the 2nd day (overclocked to 850MHz based on ideal preset), so I can't compare to a stock kernel or earlier ED versions. The only problem I have identified is that one must not upgrade libncurses5 to squeeze.