If the noise is the same with the clutch pulled in while in gear as it is while you are in neutral it is normal. There's a lot of weight getting slung around in your engine that increases with the transmission engaged; you are going to hear noises. Gear noise is something you will never get away from -- it's almost better to get used to paying attention to the engine noise which sounds much more like a sewing machine.
People that have never rode a bike with a windshield or that have only rode bikes with minimal windshields are the most sensitive to the noises. Those people are usually the first in line to upgrade their exhaust. Which is fine; it keeps the exhaust companies in business.
If you are one of those people look for the D&D group buy post from CrossRoads; he is working to try to get a reduced price -- if enough people elect to join in the purchase the price reduction could be significant.
Retired USAF, IYAAYAS!
2008 V-Star 1100 Custom Bobber project
2011 Crimson XR with Forged Highway Bars / Hard Bags / Passenger Backrest, Ness parts including Smooth Layback Plate Frame/Mount / Rad 3 Mirror / deep cut grips / drivers floorboards /shifter peg / brake peg / passenger pegs. Witchdoctor black rack, Lloydz filter / timing wheel / VFC III, 7Jurock windshield, Drag Specialties seat.