In the PlutoHome distribution there is built in checks in some of the scripts that enforce the same Kernel version on the Core and the MDs. I am not sure if this has been removed for linuxMCE or not, but it is something to look out for.
You will have to be carefule that setup scripts don't overwrite any settings changes you manually make.
If you just need a couple of config changes to the kernel, I would recommend getting the sources from the linuxMCE repository and changing that and rebuilding, rather than getting a fresh set of kernel sources.
Let us know how you get on.