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Upgrading the kernel has nothing to do with the partitions on your hard disk. You could either use apt to upgrade your kernel, or better still compile it yourself! Just download the kernel sources from http://kernel.org/ and make sure you have the correct utilities as mentioned in the README. Then proceed according to the README.
It does, ext2 filesystem specs have changed for 2.4.x. You need to add backward compatibility flag if you want it to be used with 2.2.x series AFAIK
Supreet