$filename = "MyJScript01.txt";
push(@filenames,$filename);
$filenumber = 1; #variable to track the filenames format: MyJscript#.txt where # is a number
open (OUT,">$filename");


print OUT "<script language='JavaScript'>\n";
print OUT "function whichMapper(obj){\n";
print OUT "if(obj.selectLSO.selectedIndex == 1){\n";
$lineCounter = 3; #Track the number of newlines printed to the JS file

(other code with many prints each line incrementing $linecounter)...

	if($lineCounter > 1000){
		close OUT;
		$filenumber += 1;
		$filename = "MyJScript0".$filenumber.".txt";
		push(@filenames,$filename);
		open (OUT,">$filename");
		$lineCounter = 0;
	}
	
}

	print OUT "}\n";
	print OUT "</script>\n";
close OUT;
(at the end I do stuff with the files created)...