I must chime in here.
I bought my VTX primarly for two up riding.... or so, I thought.
It goes like this. I had a shadow for a while. It was a great 750cc bike. I could take it on the express way and enjoy it; I'd go to and from work (60 miles at the time). I'd go for random rides. But, I (we?) wanted to tour. We took it (two up) to galena IL which is (given the route we took) about a 3 or 4 hour ride. We had some comforet issues and

() bathroom issues on the ride. We took back-roads because the 750cc bike barely had the power to get to a safe highway speed two up and even then it was taxed. Didn't have additional room on the throttle to speed up past 75 mph if need.
So, shortly after that I started looking at larger displacement bikes. My wife too, enrolled in a motorcycle certification course (she planned this as a surprise "gift" to me). She passed, I bought the VTX. I went on a few street rides with her on the shadow but she was never extremely comfortable driving the cycle her self. She decided against getting her lic. (because then we'd have to add her as a lic. driver on insurance and that'd raise costs). So, at that point I started making modifications to my VTX to accommodate a passenger with the intention of touring.
Fast forward two years and we've sold the Shadow this year. It hadn't been ridden except for me to ensure it kept running right or to move it. We've spent roughly $600 adding things like a sissy bar and floor boards to the VTX. More if you add her gear in (close to $1500-$2000 then). (I also spent money configuring the shadow for two up riding but lets set that aside as I chalk it up to my mistake -- should have gotten a bigger bike from the get-go).
Keep in mind, she was on board with all of this saying it was fun and she'd like to be able to ride with me. I've always discussed doing the IBA 1000 mile runs and going to the grand canyon from Chicago. She told me that it'd be great.
At this point in the year she's probably only done 25-30 combined miles with me whereas I've done close to 500 or 600 total. All of the money I've spent on modifications for my VTX thus far has been for passenger comforts; I've added nothing that I wanted like highway bars or fairing. She will now avoid riding at almost all cost citing it's not comfortable or that it's boring. I am also starting to hear about the money I spend (or want to) on it (and mind you, we have a healthy savings, two properties (one of which we rent [which is fall out from the economy]). We are in a better position then a lot of people.
So,
ultimatly my point is -- are you sure she
wants to ride or is she trying to please you? It might be important to consider this. Perhaps she is not getting the enjoyment from it you are and therefore she is citing issues to either avoid going or on the ride she is spending time thinking about it because she is board.
I don't mean to imply she "probably" is doing this or you face the same scenario I ran into. I just think it's important for you to consider and discuss with her before you invest heavily in adding things to the bike for two up riding when there might be things you'll get more use out of. Be neutral; make sure she knows it's ok if she doesn't want to do the longer trips you might be planning.... For shorter trip boots (for safety) and the pegs will be fine....