I have installed both Gentoo and Arch Linux in VMs and real hardware. Both are the most customizable Linux distros I have worked on. You basically get a bash shell and build from there. However if you really want a customizable version of Linux that you can say you built then you should take the plunge and try Linux from Scratch.
Linux from Scratch (LFS) is a version of Linux that is built completely from source. What you get from LFS is a document that walks you through how to build your system. I just finish the section where you build your temporary tool-chain that you will use the build the system. The instructions were great. So long as you follow them exactly you should be fine. I am right now building an x86_64 based system, however depending on how successful I am I may try to build a PowerPC version on my iBook G4.
I will be adding posts as I work through LFS. Document both the success and issues that may arise.