The simplest solution of all would probably be to roll the functionality of your shell scripts into you perl code.

If you can't do the above, then it may be that you're not familiar with (or haven't considered) piping, which might be a good choice for the other-than-environment-variables that need exported to your perl script.

If you are familiar with piping, please ignore the rest of this response. It's real newbie stuff.

There is a short tutorial on piping here.

As an example, lets say that your shell script outputs the lines:

fee
fi
fo
fum
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A perl script that is expecting piped input would look something like:

#!/usr/bin/perl -w
use strict;

while (<STDIN>) {
  print uc($_);
}
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If I then 'piped' the output of my shell script into my perl script with a command like
giant.sh | caps.pl
my perl scipt, caps.pl, would print the following to STDOUT:

FEE
FI
FO
FUM
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This is a very trivial example. It would be much better to have your shell scripts print identifiers for each line so that there is no question about what line belongs to what other-than-environment variable.