I haven't looked through the entire code in detail, but in multiple places you're confusing something like

  $href->{port_list}   # correct
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with

  $href{port_list}     # incorrect - assumes a hash %href
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(where the $href stands for $module, $self, etc.)

As the object is a hash reference, you need the arrow here  (you can omit later arrows as in $href->{foo}{bar}, but not the first).

#!/usr/bin/perl -l

use strict;   # !!!
use warnings;

my $module = bless { port_list => [qw(a b c)] }, "Foo";

print "size=", scalar @{$module->{port_list}};   # ok
print "size=", scalar @{$module{port_list}};     # not ok!
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without use strict would give

$ ./835728.pl
Name "main::module" used only once: possible typo at ./835728.pl line 
+9.
size=3
Use of uninitialized value $module{"port_list"} in array dereference a
+t ./835728.pl line 9.
Use of uninitialized value $module{"port_list"} in concatenation (.) o
+r string at ./835728.pl line 9.
size=
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and with:

$ ./835728.pl
Global symbol "%module" requires explicit package name at ./835728.pl 
+line 9.
Execution of ./835728.pl aborted due to compilation errors.
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Also (though irrelevant to your problem), it's a generally accepted convention to use CamelCase names for normal packages/modules, because all-lowercase names are "reserved" for pragmata (like strict etc.).