I have never had much of an issue with any upgrade I have done. The only one I can think of was 10.2.8 before they issued the fix for it. Every other upgrade (since 10.1.2) has been fine (shrug). Don't know what to tell ya...
I bet they bundle the DVD Player update into 10.4.1. They pushed iTunes 4.8 out via SU to support the new iTunes stores and fix some security holes (i.e. probably thwart the latest DRM workaround). iTunes is high visibility, so they want everyone to have the latest and greatest version ASAP.
I think the above poster thought you meant the Mac mini. One of the companies he linked too also makes this case, which I have for my own iPod mini. Works awesome! I can keep the mini, the firewire cable, and the AC adapter all in one package. When my mini is on my person, I use it for my digital camera's battery charger, USB cable, and a spare battery and SD card.
Insert the install disk and boot off it. After the part where it asks what language to use, you can pick a drop down list of utilities in the menu bar. It's in there along with Terminal and Disk Utility, and a few others.
It's encoded as Apple Lossless (ALAC) so that the stream can be sent encrypted to the base station. I have this happen now and then as well. Sometimes if the processor is taxed you get the skipping. The bandwidth on the regular AirPort (11 Mbps) is more than enough for the streaming, it's basically the processor.
I have the latest Virex (7.5.1) from .Mac on my machine (see below) and it has never caused a problem. It sounds like the Fax functionality might be suspect. If it was more random then a bad stick of RAM might be causing problem. If it begins reoccurring at random, take out one stick (don't know how easy that is with the G5 iMac) and try running and seeing if it happens. If it does, swap sticks and repeat. This is just a stab. I just generally know that random errors...
Generally speaking, subwoofer placement can be pretty flexible. The low frequency sound it produces is omnidirectional, so as long as it is placed on a solid surface it should be fine. The two satellites will be the ones you'll fiddle with to get a good soundstage. That will depend on room size and what not.
I've had FileVault on for a while through several updates (through 10.3.8 ) and never had an issue. All FileVault really affects is your Home directory (makes it an encrypted disk image instead of a folder). Non of the System files are encrypted. And if you are doing a clean install then it's a moot point anyway.