I think the core of your problems is your nested loops:

foreach $Query ( keys (%hash) ) {
foreach $Query ( keys (%hash2) ) {
   print "$Query\t$hash{$Query}[0]\t$hash{$Query}[1]\t$hash2{$Query}[2
+]\t$hash{$Query}[3]\t$hash{$Query}[4]\n";
}
}
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As soon as you have more than one entry in the hashes, the number of lines being output will multiply...  Also, it's generally not a good idea to use the same loop variable ($Query) in both loops :)