Maybe I'm thinking of it wrong, but more pre-load is a more compressed spring, and that would lower the bike more - less pre-load would raise it... but both won't change the height it once the rider's weight it factored in unless you weigh so little that even on the softest pre-load your weight doesn't compress the spring.
Why not ask your wife to go for a test ride, then hit what you always hit with it and see how it feels? If it improves, then try to reduce the preload a bit for when you ride it.
Two other things that came into play over the course of the last many miles with my Vulcan - the rear tire matters in ride quality in two ways... err... maybe three (unless someone puts on a wider low-profile tire, then all bets are off). You should be airing it up for loaded rides (you and gear, you and your wife), and lowering the pressure a bit for solo light rides. New tires vs. old, with the same amounts of tread, mattered too. I would hope you don't still have the original tires on that bike - 5000 miles or not, seven year old tires (eight if your 2005 was built in 2004) are harder and beginning to dry-rot or crack. New rubber is softer rubber. I noticed a big change when I went to a new rear tire from the new-looking (plenty of tread depth, previous owner stated they had just over 200 miles on them - and the tread depth looked that new), but old Metzler 880's it had on it to the new Dunlop I changed the rear out for. Once the Dunlop wore the ride was harsher, but I didn't realize how harsh it had become until I put the new Kenda Cruz on the rear... wow, much nicer ride!
So I'd suggest you go take a good look at your tire pressure on the rear, and evaluate the rear's age - my VN800A changed dramatically between rears for the nuances of highway bridge joints and such.
Since I noticed ride differences in the rubber compounds, I'd guess that higher-mileage rears would have a harder compound, normally, and thus give a harsher ride. The squish of the air and sidewalls isn't the only thing that matters, the squish of the rubber of the tread counts for a lot on 800's, it seems, where my other bikes aren't so touchy.
Edit: I hope you appreciate this - I set my bowl of ice cream down to type that out, but when I turned to get it I found my cat licking it. One good bowl of Ben & Jerry's down the tube
