You can grab all the possible values for intron and exon with your regex and then split them up.

Consider replacing your intron/exon elsif blocks with this:

  #new intron elsif block
    elsif(/\s+\/intron="(.+)"\n/) {
        foreach $item (split('\;',$1)) {
            print OUT "Intron\t $item\n";
        }
    }
[download]

I replaced all the *s with +s, from my understanding this is more efficient, but I'm no regex guru :) The regex puts everything between the "double quotes" in $1

This will print out, based on your input data:

Intron   1-48
Intron   334-385
[download]

Now that they are separated, you can do whatever you want with them.

Ryan