I didn't get any errors when unpacking it. I think I may see the problem. I had mistakenly put data.tar.gz in /usr and ran the tar command from there, so there's actually a /usr/usr/bin instead of /usr/bin. I'm not sure if that makes a difference or not. Anyhow, here are the results from those commands.
empeg:/empeg/bin# df /
df: Warning: cannot read table of mounted filesystems: No such file or directory
Filesystem 1k-blocks Used Available Use% Mounted on
- 15863 13949 1914 88% /
empeg:/empeg/bin# echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/empeg/bin
empeg:/empeg/bin# ls -ld /usr/bin
ls: /usr/bin: No such file or directory
empeg:/empeg/bin# ls -ld /usr/usr/bin
drwxr-xr-x 2 0 0 1024 Jul 31 11:01 /usr/usr/bin
empeg:/empeg/bin# ls -l /usr/usr/bin
total 4
-rwxr-xr-x 1 0 0 3448 Jul 31 11:01 tclsh8.4
If that is the problem, should I just try it again from the root directory?