It seems to me you've got 3 options there:

1. auto-translate;
con: GIGO ie crud shell input => crud Perl output.
pro: quick/low effort

2. Hand code new Perl modules as you go.
con: Takes a while, same cruddy architecture as original
pro: you'll get good, maintainable Perl that does logging etc. Also means you can replace shell files gradually, instead of the big bang approach.

3. Design a new/better ctrl system in Perl from scratch.
pro: Gives you better code and more integrated approach.
con: more effort upfront & big bang approach

I once had to do a FORTRAN to C job (Y2K) and we originally tried option (1.), but I ended up doing a fair bit of (2.) to make it work properly.
A straight option (2.) approach might have been quicker in the long run, otherwise you end up with weird looking code due to the auto-converter.

HTH Cheers
Chris