Before going any further, can you post some sample code of your 'flat' scripts please. Just post one or two in the original language, along with the converted perl scripts. So we can get a feel of the complexity of the scripts.
in reply to Finding duplicated code in Perl
My gut feeling is that it might be easier to eliminate duplicates from your original scripts, which you have described as VERY simple. So the idea is to eliminate duplicate from your original scripts before converting them to Perl.
Otherwise we could have a look at the complexity of the Perl code generated, and we could come up with a generic enough solution to your problem.