3.) It seems like there would be some room for improvement on this code for efficiency to speed things along, but I can't seem to find it. Any suggestions would be very appreciated!!!

Unless I misunderstood your code, you don't use %minhash for anything except creating @npanxxarray and %npanxxhash. Maybe it's possible to replace these three variables with only one? Let's see. Processing large flat files is usually done within a single loop which reads the file and does the computations, caching as little data as possible. Why not trim and count your values as you get them? Like this:

my %counts;

while (<IN>) {
        next unless /^{.*$/; # skip non-matching lines
        my $min = (split ',')[1]; # get the value
        $counts{substr($min,0,6)} += 1; # found another one!
}

# at this point %counts is like your %npanxxhash, but without all the 
+temporary variables
[download]

(code is untested, sorry)
Counting values like this will take much less time than I/O required to read the file, so there is no need to use multi-threading here.

Aside from that, child process can't modify variables in its parent, you would need to use threads and shared variables instead.