use FileHandle;
my $fh = new FileHandle;
my @input_file2;
tie @input_file2, 'Tie::File', \$fh, or die "Problem tying file $input
+_file2: $!";
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... gives...

usage: tie @array, Tie::File, filename, [option => value]... at ./SS7M
+erge line 42
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What's all that stuff with $fh? You appear to be trying to pass Tie::File a reference to a reference to (sic) a GLOB when all it really wants is a filename.

Surely you just meant...

tie my @input_file2, 'Tie::File', $input_file2
   or die "Problem tying file $input_file2: $!";
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You can pass 'Tie::File' a filehandle (aka a reference to a GLOB not a reference to a reference to a GLOB) but you'd need open it first.

open my $fh, '+<', $input_file2
  or die "Problem opening file $input_file2: $!";
tie my @input_file2, 'Tie::File', $fh
  or die "Problem tying file $input_file2: $!";
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Note, the FileHandle module was long ago superceeded by the IO::* modules (particularly IO::File and IO::Handle) but you rarely need to construct them explicitly.