With the X vesa setup you can choose the mouse config, and then back up your ~/.xsession file to be persistent. Actually, doing a backup by default will preserve the home directory where .xsession resides. I am assuming you don't have Xorg installed that is. Then it would be backing up /etc/X11/xorg.conf.
The dillo wbar issue was fixed in the repo. Perhaps the mirror has not synced with ibiblio yet if it is being downloaded from a mirror. I will double check when I get home tonight. Editing or replacing files that are part of a tce will get overwritten each time the tce gets loaded on boot. The edited file can be backed up, and the backup will be restored after the tce untars so it will persist.
For uninstalling tce's there is a tce-uninstall extension available in tce format.