The immediate thing I notice is that @Attn is way larger than it needs to be. It looks like you determine a value for each element in every 14-element slice of @in. Instead of storing that value 14 times, just store it once, and have each element of the 14-element slice of @in look to that one element. This is untested, but...

for (my $i = 0; $i < @in; $i += 14) {
    my $num = $in[$in[$i+12] * $MaxAgc0;
    push @Attn, $num / $in[$i+10];
}
for (my $i = 0; $i < @in; $i += 14) {
    foreach (2 .. 9) {
        push @powers, ($in[$i + $_] - $Attn[$i/14]) / 100;
    }
}
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Actually, now that I wrote that out, I'm thinking you don't even need to build @Attn (again, untested):

for (my $i = 0; $i < @in; $i += 14) {
    my $num = $in[$in[$i+12] * $MaxAgc0;
    $num = $num / $in[$i+10];

    foreach (2 .. 9) {
        push @powers, ($in[$i + $_] - $num) / 100;
    }
}
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EDIT:

All the above code may be wrong. I misread what the j-loop was doing in the original code; I had thought you were comparing to a slice of @in for some reason, but that's apparently not the case. I'm confused though...does the input data provide some sort of meta-information that you're reading in at every 14th element?

My initial thought was that @Attn and @in were meant to be parallel arrays, but with the limit of the j-loop being defined that way, this would probably not be true...