I never found good documentation on upgrading/compiling linux kernel in Debian, Most of the time I stuck in between and my running libs gets corrupted, then same story; Put new hard disk, Install latest Debian, mount old HDD and copy all the contents.

After reading documents in net, I setup my step-by-step Linux kernel up-gradation (Bash Scripts) in Debian. Up-till now I upgraded more than 5 Debian kernels without any problem.