Split the logic in line 311 into multiple lines (i.e. different ; separated statements!) for debugging.

I'm not sure if Perl's warning message can be customized this way. LanX's suggestion would probably help in that regard. See perldiag (emphasis mine):

Use of uninitialized value%s

(W uninitialized) An undefined value was used as if it were already defined. It was interpreted as a "" or a 0, but maybe it was a mistake. To suppress this warning assign a defined value to your variables.

To help you figure out what was undefined, perl will try to tell you the name of the variable (if any) that was undefined. In some cases it cannot do this, so it also tells you what operation you used the undefined value in. Note, however, that perl optimizes your program and the operation displayed in the warning may not necessarily appear literally in your program. For example, "that $foo" is usually optimized into "that " . $foo, and the warning will refer to the concatenation (.) operator, even though there is no . in your program.

Does your code treat undefs like the empty string or 0, or do you treat undefs differently? If you treat them differently, you'll have to put logic at all the appropriate places to handle them. If not, then one solution is to change all undefs to the empty string or 0 at the point where your data structure is populated, e.g. $hash{$foo}{$bar} = $value//"";, or later on, e.g. $_//=0 for @values;. Or you could say no warnings 'uninitialized';, but then you might miss mistakes in some places.

To build on LanX's note:

     $test1 = $test2 = $test3 = 6;

Is better written as

     use strict;

     my $test1 = 6;
     my $test2 = 6;
     my $test3 = 6;

Or even better as

     use strict;

     my $DEFAULT_TEST_VALUE = 6;

     my $test1 = $DEFAULT_TEST_VALUE;
     my $test2 = $DEFAULT_TEST_VALUE;
     my $test3 = $DEFAULT_TEST_VALUE;

And clever you -- you just stumbled onto one of the many, many, many reasons why.

That said, the if(!defined($var)) approach is about as graceful as it gets, although you might be able to make use of the new-fangled // operation to save some typing.