I was facing a lot of grub problems which couldn't be solved otherwise, and hence reinstalled. But to keep my old software, I did not format the usr n opt for which I've separate directories. Afterwards, I mounted them in their positions and edited/etc/fstab to get back my previous state .. of course I had to install mono again, since I guess it's stored in bin, lib, et al, rather than usr/bin, usr/lib, et al .. every software is working perfectly as expected. However, I had no idea that the dpkg stuff aren't stored in usr. (/var, /etc was & is in the same partition as / ) Hence, I can't upgrade my kernel or other stuff .. is there any way to make apt-get check all the software in usr and update it's lists, and maybe correct the dependencies of they are available under the repos in /etc/.../sources.list? Of course, I must add the required ppas, and reinstall stuff outside usr, such as some compilers. Furthermore, just a suggestion in the wrong place I believe, can't there be 2 or more extra lists, in usr & under /, which store the names of the packages installed under it, and cross location (in or out of usr) dependencies, so that apt-get accesses them such that in case someone does something like what I did, apt searches the list and updates it's main list?
seems like you messed up your installation with the reinstall, there are complicated methods to fix this, and yet you might end up with a broken installation, which would be very susceptible to future version upgrades, i won't advice that, given that i tried them a while back and its kind of more work than output, hence keeping usr or other dirs from old installations in not very "cool" so as to say, for reinstalation i now maintain a script of all the stuff(pkgs and repos) i need in a script file and run that after a reinstall, i only catch being you need to have an unlimited(so as to say) data connection.
the simple redundant process would be a complete re-installation, for the grub related problems i'd advice you to get to know grub installations or in case of a dual booting sytem use grub4dos which is much simpler, from a usb live system or checkout the gui distro http://sourceforge.net/p/boot-repair-cd/home/Home/ or boot-repair in general,