They still have stage 1 and stage 2 documentation available, there is a link from the stage selection page on how to do it.
IMO, doing a stage 3 and then, after getting everything like you like it do an emerge -e system && emerge -e system.
That will optimize everything to your liking, and be no different than what a stage 1 will do.
The reasoning behind going with only a stage 3 for the main docs (besides all of the support questions) is that when you do a stage 1 or 2 is that your toolchain isn't complete (from what I have read, I never had any problems with it). But anyway, I did a stage 3 for my past 2 installs, and I am really liking it better. You can still optimize (not that the optimizations were that great on new hardware anyway) and you still have a very stable system.
I don't run gentoo because of the optimizations, I run gentoo because of the ease of administration, the support forums, and I don't mind waiting for things to compile.
Another question though. Why all the distro hate? (mainly between debian and gentoo) What is wrong with different people liking different things? I always thought choice was a good thing? I have tried them both, and just prefer gentoo. Nothing against debian, it is a great distro.