You're doing the right thing - it sounds like you need more data.
Personally, I don't think a Skipper's handicap will ever work, simply beacuse you can't track people swapping boats. Besides, depending upon the course set, how well a boat does often has very little to do with the skipper and more to do with the crew - fast kite hoists, quick tacks, no foul-ups, etc.
The system we use for Classic Yachts over here - where you can have everything from +50' Gaffers to 26' Folkboats racing together - is a straight time-based Performance Handicap, and there is well-proven software available that will do all the hard work for you:
Top Yacht Software
The web site isn't flash (personally, I think the people there are too busy doing real work), but the software geniunely IS used for both club local and major race events all over the world.
I hope this helps.