Step one, check all of the code into a reliable version control system. Accept nothing less capable than Subversion (darcs, git, bzr, svk, and p4 should all be fine). If you don't know how to use a revision control system, learn.

Step two, run Perl::Tidy over all of the code per your preferred rules. Check in the new versions. Make sure they still compile with perl -c and check any perltidy.ERR files.

Step three, Perl Medic should have arrived by now. (Order it as step zero. Do not skip this step; it is an excellent book written well by a very capable programmer and everyone should read it.) Follow its steps.