Your Pentium D will be fine and you will need a running kernel to build another one but a liveCD will provide that.
You have two options ... do a 486sx compatible Gentoo install on a real partition on your Pendtium D host system
With some care you will be able to boot into it and test most of it.
... do a 486sx compatible Gentoo install into a directory (or a file) on your host. You will not be able to boot this - you will have to chroot into it
Either way allows you to build a kernel and anything else you need. You also get the binaries you target system needs. You can leave behind the sources and the toolchain whe you install on your target since you will never build anything there.
The install you need pretty much follows the Gentoo Handbook
but keep in mind you are installing for your target not your build host.
You will need the x86 stage3 tarball, (not the i686 tarball).
This won't mean much yet. Be sure you set FEATURES="buildpkg" in your /etc/make.conf so the install process saves all the packacges you build. That way they are all ready for your target.
Follow the handbook about setting up /etc/make.conf
After you have your stage3 and portage snapshot, update it with
If in doubt ask - here, on the Gentoo forums or in #gentoo in irc.freenode.net. This is a fairly standard approach for building Gentoo on one (more capable) system where its intened to run on another less capable system.