I am not following why you needed to create the temp hash. My output appears to be correct for the example given with the following line of code.

for(@mips){$hash{$_}||=999}

UPDATE:
Thanks crazyinsomniac, after reading these posts several times and talking with you in CB I realize that the example above did not have G in it once it was processed. I read the question and did not examine the output. In the text of the original question it does not state that missing keys should be removed, it merely states that the values should be 999 if they have none.