5'4", about 120lbs.
I would also look at lowering the bike....max is 30mm from what I have found...and softening the suspension, probably to its lower limits.
I think your best bet will be to go for a smaller bike. With all the mod's you're contemplating, it would be impractical. I doubt you would save any money either.
You can only retard the timing so much before the engine runs too roughly. And although it is easy enough to load up different maps you have in your possession, a custom dyno tune will still cost you about $300, the power commander modules are $200-$300 as well.
The insurance for a new rider on a litre bike may be quite high too, at least compared to a sub 600 cc bike.
as a rider with more experience now, you also have to continually remind yourself that your wife who has zero experience does not have the throttle control you've developed, and this lack of control (and not lack of caution) is what tends to get new riders into trouble.
Also, the 10R will have a more race tuned handling set-up. This precision handling, although a delight to more experienced riders (because they have developed a greater sense of finesse in their control) actually becomes more of a detriment to newbies as the "over-responsiveness" tends to make them lose confidence. It's the same reason newb skiers and snowboarders are given softer "less responsive" skis or boards.
As for weight, even a 50 lbs weight difference is significant when dealing with motorcycles. 50 lbs is not exactly light, not for someone who only weighs 120 lbs to being with. Not knowing how strong your wife is, it may be the difference between dropping the bike or not, or being able to pick it up once it's dropped. It's also not just the total weight of the bike you need to consider, but also the distribution. It's been my experience that if the centre of gravity is lower, the bike tends to be more newb friendly.
putting a restrictor on the throttle may seem like the easiest thing to do, and it will definitely limit power. It is my understanding that the bikes owned by FAST riding school are restricted this way for the sake of safety (ie. you can't turn the throttle to full factory wide open). I'm just not certain it will be enough to make up for the other factors I've mentioned above.
And lastly, lowering the bike 30mm and then softening the suspension as much as possible seems like a recipe for bottoming out. If that happens while cornering, it will very likely lead to a crash. It may also lead to damage to the bike, as Draco's Wrath found out the hard way (he has a thread posted about it). Also keep in mind that lowering the motorcycle may void your insurance. It does with TD Primmum.
i'd say bite the bullet and get a ninja 250 for the wife because that would seem like the safest, most practical route.
hope that helps.
btw, that MV Agusta F3 is pretty sweet. I can't believe it is priced at $13,500 for sale in the USA. Having said that, I still don't think a newbie should have that as their first bike.