.40 for 1999 is correct. 1996 - 1997 is .38 and 1999 and newer (2004??) are .40.
Five inches of sag is way too much. Please lose 30 - 40 pounds and report back with your new sag numbers, or just get stiffer springs. :-)
When you are sitting on the bike, the general expectation of sag is around 25%, I believe, which is around 3" if travel is 12".
Generally, once the sag tells you that you have the correct rate spring installed, then it is time to work on valving.
cc is out and about. He even shows up on TT sometimes!!