1) I use [link|http://subwiki.honeypot.net/cgi-bin/view/Main/DebianKernelBuilding|http://subwiki.honey...ianKernelBuilding] for my kernel building needs. Had no issues with it other than with initrd.
2) Debian saves the kernel config in /boot with the kernel. Diff it to see what may or may not have been left out of your new config.
3) Are you using grub? And did you save your old kernel?