1. There's no reason to explicitly skip words less then 4 characters. if it's less then four, shuffling the "middle letters" will either be a shuffle of one, or zero characters.
2. This doesn't solve the problem exactly as you described (your requirements about comma,period are pretty specific, and don't cover other punctuation), but it's pretty close...

   #!perl -p
   use List::Util 'shuffle';
   $_=~s{(?<=\b\w)(\w+)(?=\w\b)}{join'',shuffle split//,$1}xeg;
   [download]

   It's by no means a good Golf ... but it's a good starting point.

perl -MList::Util=shuffle -pe '$_=~s{(?<=\b\w)(\w+)(?=\w\b)}{join"",sh
+uffle split//,$1}xeg;'
[download]