For the most part, you should be safe with the Wee for the purposes you want to use it for. What you describe is pretty much exactly how I've have been using mine, (for all of one season). Made a few multi-day trips with my wife perched happily on the back. She gets so relaxed that sometimes I have to make sure she is awake to be sure she doesn't roll off!
We have Givi top and side cases for storage. Cases of any kind make passenger mounting a bit challenging, I think due to crowding the pegs, but once seated, all seems well. We have not bothered with a back pad on the top case though. Partly to give a bit more passenger room, but it also seems a bit redundant, given the padding in the back of her jacket.
The Givi rack for the top case has worked out well for us, but if you search here you'll find there is another rack..I think from Adventure Motostuff, that would allow you to shift the case position back at least an inch or so. That could buy you some critical space. Can't advise anything on modifying the passenger peg position. Haven't needed to look into it before. Fortunately my wife is about 6 or 8" inches shorter than yours. Either way, the Wee has got
to be a lot better than the SV650!
Two places to check for accessories/modifications would be the afore mentioned Adventure Motostuff and Twisted Throttle; ( http://www.amotostuff.com
). I've no connection with either. That's just somewhere to start for you.
Good luck with the search.