Based on a little experimenting with a normal user account on my box, it looks like CPAN loads either the global configuration file or the local one.

I suggest copying CPAN::Config to your local directory (~/.cpan/CPAN), modifying what you want to modify, then running CPAN interactively.

I removed everything but the build directory from MyConfig.pm, and it prompted me to fill in the rest of the values. The defaults were pretty sane, though.