Can I flash a custom ROM and a separate custom kernel after?
Yes, flashing a kernel is mostly safe. The worst thing that could happen would be a boot loop aka soft brick, which can be fixed by flashing another, proper kernel.

Remember that the kernel in your case has to be CM (CyanogenMod) compatible because Resurrection Remix is built on CM. There are many different kernels, so look for the one that matches your needs (performance, stability, battery life).

XDA developers helps with titles (look for [KERNEL] in the title) and the XDA DB gives you a quick and easy way to find kernels and ROMs you want.