jonmchugh,
Nope...nothing that you do with your /sdcard (other than apps2sd) will affect your root status. Good choice of PlainJaneT2, by the way.
When you flashed the custom ROM, it was installed (flashed) to your phone. You actually don't need it on your phone anymore if you need the space and don't intend on re-flashing it for some reason. You should be doing Nandroid backups (i.e., before flashing a new ROM) however, and they are stored in the /sdcard/nandroid directory on your /sdcard. They can take up to 250MB of space. These too are not needed for normal operation of your phone and need only be present when (if) you ever use them to restore.
You can safely copy these files off to your computer or other disk should you choose.
Cheers!
edit: okay, eu1, this time you beat me, lol!
off-topic / not related to this thread (apologies): I actually came back to my computer to make sure that my app was properly calculating the MD5 sum for the file in question in the other thread (eddie's trackball issue) and to make sure that he wasn't seeing an SHA1 checksum.