I started with yggsdrasil, too. I got it, a FreeBSD CD and a CD full of lesstif applications from Walnut Creek.
This was back in the days when more people didn't have CD-ROM drives than had them.
I started with BSD, with the understanding that it was closer to the SunOS 4 stuff I was using in class. And it was, but it didn't support the 2nd CPU in my workstation (yes, I had an SMP 486.), and my attempts at building my own kernel resulted in something that just wouldn't boot, even though it compiled correctly.
I tolerated BSD - it handled internet stuff better than OS/2 2.1 or NT3.1, after all, until the end of a semester, then pulled out the yggsdrasil CD.
The install off the CD was pretty bad, but once I got it running, I had something that was at least as functional as BSD. Once I got it online to start grabbing updates, though, I knew I had a winner, since even back then (.94, maybe? I don't think it'd hit 1.0 at that point), there was work on an SMP branch for the kernel.
I submitted bug reports and re-built about once a week, pretty faithfully until I ditched my 486 and later Pentium SMP rigs for a PPro 200.
As far as OS files, yes, it bugs the hell out of me. More with Windows than Unix, since everything ends up dumped in just a couple of directories (Why the hell is this stuff from Symantec in my OS libraries folder???). Making stuff from source on a *nix machine, things go in /usr/local/, which normally tells me right away that if nothing else, I probably don't need it.