How to check the running kernel version

This is no actual answer to your question, just a pointer to a tool that might be related and helpful:

Do you have dkms installed? (Some information here, the alioth page seems down at the moment.) It's supposed to do just that, if I'm not misled. It requires the appropriate linux-headers package and the module/firmware/something-like-that package to be installed; and it works for all installed linux-image packages. (I can't say anything about a generic module, but it worked fine when I used it with the non-free nvidia module.)

(There're more links here, like the manpage and this linuxjournal.com article which provides a non-Debian-ecosystem-centric explanation of the program.)

3.x is just continuation of 2.x - at one point Linus decided that the "x" part of the version is too big. Generally you probably want reasonably recent kernel, probably one marked as "longterm". A lot also depends on your application as well - while remote security holes in kernel are rather scarce, local problems are much more prevalent.