First of all, great choice going with the Yamaha FZ-09 for your second bike! This sounds like the perfect bike given the format and price range you were looking for. Personally, I would crown the FZ-09 the “Bike of the Year” award for the best all-around package offered in the 2014 model year. The beefy power plant, comfortable yet aggressive ergonomics and impressive electronics package make for a ride that hits the mark on so many aspects. With some aftermarket suspension and an upgraded breaking setup (perhaps cross-compatible parts from the FZ6, R6 or R1?), this bike could be unstoppable. Did I mention the sticker price roughly 30% below its intrinsic value??
As for your comfort issue at freeway speeds, this could be rooted in a couple of causes. First, as you suspected, the naked bike format with wide, dirtbike-style handle bars do not create a very aerodynamic situation when air resistance begins to come into play. Your Thruxton does not have much in the way of fairings to reduce this effect either but it does have lower-mounted, sweeping bars (similar to sportbike clip-ons) that naturally put your body in a riding position less reminiscent to that of a wind sail.
An aftermarket windscreen would be the best remedy to this problem. The trouble is, not many manufactures or distributors have a wide variety available for the relatively new FZ-09. Yamaha Genuine Accessories does offer a front cowl but this seems more like an aesthetic addition than functional upgrade. A true windscreen such as the products offered by Puig, MRA, Givi and Rizoma would produce the best results. The craftsmanship and quality of Puig products I’ve worked with in the past would have me leaning in this direction
A second problem that could be generating this uncomfortable helmet situation is the headwear itself. It is an extremely common occurrence for riders to wear helmets that are either too large for their head and/or not designed for their head shape.
For example, Arai helmets are generally better for people with rounder heads while Shoei’s seem to fit those with longer, narrow head shapes. Additionally, it is advised to try helmets on with the cheek pads removed in order to get the proper dome fitment. All too often riders believe the cheek pads are too tight against their faces when trying helmets on and go with a size too large. This padding is not meant to be extremely comfortable but to be as tight as you can tolerate since this is what is securing the protective apparatus to your head as you approach triple digit speeds and beyond.
In general, I have seen that both the Shoei RF-1100 and 1200 models along with the KBC VR-4R helmet work very well for the majority of people. Both of these helmets (along with being moderately priced) have excellent cheek padding that mold to the contours of the rider’s face and under the jawline securing it in place. The key here is to select the proper size, typically a size smaller than most would guess.
I hope these tips help in your quest to adapt to and maximize the enjoyment out of your new ride. Please feel free to let us know if these or any other avenues enable you to develop a solution. Ride safe and try to keep that FZ-09 front wheel on the ground!