Updated text, there is also a few other things worth mentioning for anyone wanting to use this.
There is another script I made, not incorporated with the perl as above, just a simple shell script. It takes all the pmwiki files (in my case were mentioned Main.Whatever) and translates them into a lower case version of a txt file (whatever.txt). This is meant to be done after the initial conversion, and so far most of it works to perfection. Few exceptions, like (:linebreak:) and %3c, but those are easy fixes.
Enjoy
#!/bin/bash
#############################
# PURPOSE: Strip the directory to make pmwiki files
# into dokuwiki files (lowercases too!)
# AUTHOR: Jason Cameron
#############################
grepLoop=`ls ../textFiles/ | grep .txt`
read -p "What is the directory for these files? (ie:Main.-.txt): " wikidir
for grepecho in $grepLoop
do
newwikidir=`expr $grepecho : "^$wikidir\.\(.*\)" | tr [A-Z] [a-z]`
mv $grepecho $newwikidir
done