As far as I know the upper fairing height is the same on 98 to 2009.
The center bracket changed mostly because of the radio caddy which is part of the center bracket.
The buffeting is from the air that come from UNDER the upper fairing and the best cure is putting on hard fairing lowers.
Changing the windshield height doesn't make much difference in buffeting.
If you change the fairing support brackets you should consider using the 2010 brackets and then you can use the 2010 vented fairing lowers which will cut down the buffeting around 75 to 80%.
When I raised my upper fairing on my 08 it didn't make any difference on buffeting when riding without the fairing lowers.
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08 FLTR candy red sunglo,with 2015 103 HO, V&H Dresser Duals with Monster Rounds, Power Vision tuner, Willy Shiny Wheels and Forks and a bunch of other stuff.