You're only iterating over hashes, not using the lookup features. If you do it properly, you'll increase the speed of the loop roughly by the number of elements in %hash2.

while(my ($key1,$value1)=each(%hash1)){
while(my ($key2,$value2)=each(%hash2)){
    if($key1 eq $key2){
         ...
}
}
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Should be better (and faster!) written as

while(my ($key1,$value1)=each(%hash1)){
    if (exists $hash2{$key} ) {
         my $value2 = $hash2{$key}
         ...
     }
}
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Also note that this code:

foreach(@allhits){
    while(my $str=<FH1>){
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exhausts the <FH1> iterator for the first value in @allhits, and does nothing for the subsequent values - probably not what you want.

Likewise I don't see how you ever get items into @file2. (Update: I should have looked more carefully)