There is a difference between installing the source code and updating.
If you install the source code as part of the minimal install, you will have the exact source code that was used to build your minimal system. Then you simple can compile a custom kernel .
If you installed the source code and then updated with c(v)sup or whatever, you will have source code incorporating changes made after the release of your minimal install.
In this case you will have to read that UPDATING file and
make buildworld before compiling the kernel.
I would do the GENERIC kernel first, and just follow the remainder of the steps outlined in chapter 24 of the FreeBSD handbook.
This will result in a system where the source code and the binaries are in sync again. That is the moment where you can compile your custom kernel. Capice ?
There is no secret knowledge, which only the initiated receive from the FreeBSD high priests. It is all written down in the handbook.
