'11 Roadster here with RamAir, TORs and stock headers. I'm getting 33 MPG on long highway trips and 28 MPG in mixed commuting. When the bike was bone stock, the numbers were only 1 MPG better.
Based on the good MPG you had when stock, it sounds like the speed limits in Virginia are lower (or better observed

). Perhaps the new header pipes shifted your optimal power band higher in the RPM range, and you're seeing a relatively bigger hit when cruising along at lower RPMs. Another possibility is that your tune is overly rich for your combination.