[Will Ludington]

I am running 10.5.8 and have most of the same warnings as you from Repair Disk Permissions:

Warning: SUID file “System/Library/Filesystems/AppleShare/afpLoad” has been modified and will not be repaired.
Warning: SUID file “bin/rcp” has been modified and will not be repaired.
Warning: SUID file “usr/bin/quota” has been modified and will not be repaired.
Warning: SUID file “usr/bin/rlogin” has been modified and will not be repaired.
Warning: SUID file “usr/bin/rsh” has been modified and will not be repaired.

I have not installed any additional/alternate hardware.

Apple Support recommends this article for warnings you can ignore in 10.5.1:
https://support.apple.com/kb/TS1448?viewlocale=en_US

also see:
https://discussions.apple.com/thread.jspa?threadID=1304471

The articles/threads do not list the above warnings that you have as ones to ignore, but the article might not be current for 10.5.7

Hope this helps you narrow down where your problem might be coming from.