You cannot race one-design in a Hobie 18 class using non-stock sails. There is no handicapping in a one-design class. Many one-design classes allow you to buy your sails from whatever source you wish, and you are class-legal as long as your sails measure in. But this is not the case with Hobies and other one-manufacturer boats -- you MUST use stock sails in order to race one-design. In your case it sounds like you are always going to be racing in open class anyway, on handicap, so this is probably not an issue for you. But you might want to hang onto your stock sails just in case you are at a regatta with a bunch of Hobie 18's and you want to race with the class.
Buying non-stock sails may (or may not) make your boat sail faster. But racing one-design will make YOU a faster sailor.
P.S. To answer one of your questions, when you are racing on handicap, the rating given you through US Sailing is the one that is used at all levels of racing. It is based upon the modification factors supplied with the Portsmouth yardstick. If you have a question about how those factors were applied in your particular case, you should contact Darline Hobock,
hobockd@aol.com The interesting thing about modification factors for sails is that it doesn't matter whether they were made by Randy Smyth or whether you sewed them yourself using Martha Stewart bed sheets.