If you're just changing out the kernel, do this after unpacking and/or patching the kernel:
Code:
cd /path-to-your-linux-source-code
zcat /proc/config.gz > .config
cp -av .config ~/PRODUCTION-KERNEL-CONFIG
make oldconfig
make menuconfig
# Here, you can make other changes.
The other changes is where you might have issue. Basically, the crypto part of kernel config doesn't know which crypto you want to use with cryptsetup, for instance. Therefore, it's not going to auto-select all of the crypto dependencies for you, just what other parts of the kernel need. So if you have an aes-xts-essiv:sha256 LUKS partition, and you compile out any of AES, XTS, cipher chains, or SHA256, chances are that the kernel will panic when you try to mount the LUKS partition next time, especially on boot. So try not to mess with the "Cryptographic API" section without being willing to test and reboot to an older kernel if necessary.
In fact, it's best to look at these settings first as well as the settings in the LVM/RAID menu and be sure they're compatible after you're done changing things elsewhere.