I'd try something like this (untested):

# skip rule if item is an actual file or directory
# (like images or stylesheets)
RewriteCond %{SCRIPT_FILENAME} !-d
RewriteRule ^(.*)/?$ /cgi-bin/index.pl/$1 [L,QSA]
[download]

Your script can get the $1 parameter from $ENV{PATH_INFO}, and use that to determine which template file to use, etc.