I bought a GIVI top box a few years agao. It seems like good quality and works very well. No guarantee but I think this is mine
http://www.twistedthrottle.com/trade/productview/603/69/I also looked at the Shad cases which seemed ok as well but the Givi name sold me.
We were just in bermuda which is a scooter-palooza. All the locals have trunks, probably 50:50 Givi and Shad - smaller than mine but they all looked fine despite pretty heavy use.
You need a rack for the trunk of course - I assume there is one for the Bonneville SE.
I've had a few windscreens and settled on a memphis fats but I don't know about the fit for the SE. The best I had before that was a slipstreamer viper which mounts to the handlebars.