I'm not positive, but I think the kernel sources you get on Debian via apt-get have special 'debian-only' patches applied, and the latest kernel sources after 2.6.2 don't have much new hardware support. That said, on debian you can apt-get kernel-package (if you're on an intel x86 you might need bin86 too). It gives you the neat ability to create a .deb kernel package that you can install like any other software. (This is the ONLY way I have ever managed to get a kernel and modules to all work). With kernel-package after you configure your kernel just run 'make-kpkg kernel_image' in the linux source directory and it'll create the .deb file in /usr/src.
For menuconfig you need ncursesX.X-dev and tk4X-dev, but that's all I know about your configuration troubles.