Hi! I later discovered what the problem was when I tried to get my net up in recovery mode and couldn't load the right modules. Looks like somehow I ended up with a bad or nonexistant modules.dep or modules.dep.bin or similar, the fact is that the kernel modules were not loaded, this seems to be what caused all the trouble.
Running modprobe -a from the new kernel on recovery mode solved all the problems and X is working ok right now as well as the mouse and the keyboard, so everything looks fine. So... trying to see what had happened I came up with this... I had installed linux-image-4.9.0-2-amd64/testing and did: apt-get install linux-image-4.9.0-2-amd64-unsigned/unstable which removed the kernel from testing and left the configs around. I later purged the configs from the kernel from testing with dpkg --purge installed the headers from the new version and rebooted. I believe that it was the purge that messed the depmod info. I don't know if we should close the bug or we should investigate more on what happened. If you want me to investigate anymore just let me know. Regards. -- Manty/BestiaTester -> http://manty.net