Even though I still consider this Apple's problem and they don't (whoever heard of trailing periods on domain names?), I have found that updating my version of Dan's Guardian content filtering from 2.8 to 2.10.1.1 has a workaround in it, and at least lets me access the iTunes store. I'm still having problems accessign the iPod touch updates, but haven't debugged this yet.
In case you are in the same boat as me, running the IPCop firewall with CopPlus add-on (Dan's Guardian), the latest CopPlus release (3.02) is bult using Dan's Guardian 2.10.1.1, which addresses those pesky trailing periods. I just uninstalled the old version of CopPlus (2.2), and installed the latest version (3.02), and things were happy. The directions at
http://home.earthlink.net/~copplus/ were sufficiently clear. Thanks to everyone's help with working around Apple's problem!