I'm not really a Perl expert yet, so please bear with me if my advice on this question is irrelevant, or worthless ^_^ I'm just trying to help ya out, Gremlin ^_^! Ok, well, I think the way to run it (at least the super basic way to run another script from that one,) would be simply using subroutines to call that next script as the example below shows:

while ( ... 'whatever here'  eq 'whatever') {
     #all you would have to do is have a pointer to that next .pl file
+ you want to call, have a subroutine in that other file that you can 
+call from this one.  All of this is without using CGI.pm, but that's 
+ok, since this is just basic stuff, later you can learn about that if
+ you want to.     
      
     doThisSubroutine;  #this would call the sub that has your next fi
+le pointer
}
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Hopefully I understood your question correctly... if not please let me know, so I can know how to answer your question better!! ^_^ Hope this helps!

bladx ~ ¡muchas veces tengo preguntas!