If you compile a new kernel that won't change modules.conf. You'll need to edit that manually, but if you compile your hardware in as modules you shouldn't need to edit it since you'll still need the modules loaded for your hardware to work.
If it seems to be running slower than before, chances are you compiled an incorrect module or something and while it's working, it's not using your hardware correctly. Either that or the old kernel was compiled for i686 but you compiled it for generic x86 or something like that. Did you go through a read all the descriptions for the options? It sounds like a lot but you really need to do it to get a good idea of what you're building exactly.