Yeah, not much storage compared to earlier pre-gen models. I just have toolbox and registration papers in there and that's it. I actually used that toolkit once on group-ride when I had to remove fairing-panel to tighten radiator hose-clamp. Search for rack or cargo-box here and it may bring up some options. My wife's been bugging me to install top-box for while, might make custom-rack for that soon.
I've got 2008 commuter and 2009 race-bike. Seat on racer has thinner and harder foam. Not sure I notice difference in comfort. But then again, I sat on bare carbon-fibre seat on for 15-years while racing bicycles.
Might want to try padded cycling shorts to see if that's more comfortable. Also all sorts of shorts with gel-inserts and padding. Maybe double it up with gel-seat cover too!
I'm pretty sure after month of riding, you won't notice it any more.