I am not sure you understand the data structure that you want to see as output. The code you have given is not what you want. Notably you are saying push @{ $userData{$ACTNUM} }, $ref = $line;, which will overwrite $ref with the entire $line before pushing it onto $userData{$ACTNUM}. I think what you really want is something more like this:

push @{ $userData{$ACTNUM}{$ref} }, $line;
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Now having done that, you must realize that $userData{$ACTNUM}{GCA} now contains a reference to a list of all the lines where $ref was "GCA". Which means you want something more like this to access it:

for  $ACTNUM (sort keys %userData) {
 for my $line (@{$userData{$ACTNUM}{GCA}}) {
  $ACCTNUM = substr $line, 11, 9;
  $FIRM_ID = substr $line, 660, 1;
  $CURR = substr $line, 661, 3;
  ...
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That is, you must now loop over all of the lines for every $userData{$ACTNUM}{$ref} to process their (possibly) multiple values.