Problem 1: I want all the numbers to line up when printed out.

The values could be 1, 2 or 3 digit numbers. My script is a CGI, so Im guessing I want to use printf qq(stuff here) but am not sure.

printf may not be useful to you here as (I think) you're outputting HTML, so whitespace will be ignored. Have you considered using a table?

Problem 2: with one of the keys I must iterate over the multiple values in the array separatley so I can set each of them as a hyperlink pointing to a different page.I emptied the multiple values into a new array (dereferencing ?) like this:

@values=@{$hash{$id}};

Then I used a foreach to go through the array. I was surprised to find loads of extra whitespace appearing. ie. I put into the values:1 2 3 4 5 6 etc. and out came:1(1 blank space)2(2 blank spaces)3(3 blank spaces).

That's almost certainly going to be a problem with the code you're using to display the data. Can't help much without seeing it.

Problem 3:I also have a problem (unless I turn strict off) when I try to print something for which there were no values pushed in. I was hoping in these situtations just the key would be printed.

Then only print the values if they are defined. Something like this:

foreach (keys %hash) {
  print "$_ : ";
  print "$hash{$_}" if defined $hash{$_};
}
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