I think that trying Gentoo or LFS is overkill.

What OP is talking about is just compiling from sources and resolving dependencies oneself. Compiling from sources is possible on any distro (though I do think Slackware is good recommendation); package managers are tools of convenience.

Here's a good article on how to compile from sources:

http://www.tuxfiles.org/linuxhelp/softinstall.html

Note that package-manager-centric distros may not by default include all the libraries and tools you need for compiling--you may have to use the package managers to download stuff like the compilers in order to compile from sources on some of them.

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The Filesystem Hierarchy Standard (FHS)'s guidance leaves room for judgement when choosing between /usr, /usr/local and /opt. Originally it was common to use /usr/local for anything installed after the OS. Then there was much debate about whether /opt or /usr should be used. /usr now seems more popular than /opt. Few packages now install to /usr/local. A good number of products publish source that still installs in /usr/local by default though.

The target directory hierarchy can normally be set when running configure, by something like ./configure PREFIX=/usr.

One useful technique is to install into a temporary directory so you can see what will be installed before it (perhaps) overwrites existing important files or, more likely, puts files in places you don't like. Another advantage of this technique is that you can easily generate a list of files that will be installed for use when a) checking if any of them already exist and b) when uninstalling.

Another good place to look, in the absence of much documentation on building from source, is a SlackBuild, especially the script. I don't suggest that because I'm a Slacker but because SlackBuild scripts are:

• Easy to download (search for a package on slackbuilds.org), scroll down to "Individual files" and click on the *.SlackBuild link)
• Minimal so a) relatively easy to understand and b) address the essentials.

For completeness you might like to find a SlackBuild with a doinst.sh -- run during package installation, typically to install config files without clobbering any existing ones and to update caches.

Incidentally, you may also like to run makewhatis -w to rebuild the man pages database after building and installing from source.

personally, my best experience in building up a system step by step, module by module, programm by programm, is using www.tinycorelinux.net
You can load programms/modules from a very small/basic system into a full distro (it takes time).
For embedded, use perhaps "buildroot" ?
Hopefully that answer helps.