Hi Tamlane -
Why have you got your heart set on the XR650R particularly? (especially for her) as it the modifications you are considering will reduce some of it's greatest attributes - that is the off-road performance and ground clearance!
The 650R is a fantastic machine, but it is essentially an open-class race bike, so not the ideal choice for an overland tourer - especially if you are planning to go RTW. Yes the bike is awesome everywhere, and especially off-road in the desert and on trails... but it's not really suited to slogging long distances on the tarmac at a constant throttle for example... which is going to be a proportion of your trip at least.
Fundamentally, the oil capacity is only 1.7 litres, so what little oil there is is working hard. Ideally you'll need to change the oil at least every 1500 miles (not tricky in itself, but disposing of the used oil legally/conscientiously can prove to be a faff).
Also, the luggage capacity is not the greatest - of course any bike can be modified, but other than a very expensive pannier rack from African Queens (that is if they still make it), you'll be looking at a custom fabrication. Sure you can travel light, but if you are going all the way around the world that will mean taking a wider range of clothing/camp kit at the very least - unless you are going to ship stuff ahead and back home of course...
You mention the electric start. I'd suggest that if your partner is going to have problems with the height of the bike, then she is certainly going to be in trouble trying to kick start it fully laden with luggage, especially if it's been over on it's side in the dirt. There is no cheap way around this - Baja Designs have stopped producing their 'cheap' kit, as it didn't work. In fact the only one that does is the Boechat kit from XRStuff in the UK. You have to decide if nearly 2500 pounds is worth it to kit out both bikes...?
Security may or may not prove to be an issue - the 650R has no ignition key or steering lock as standard. Of course these are not failsafe on any bike, but a handy deterent if you are away from the bike briefly.
Buying smaller wheels will typically mean getting a set of 17 supermoto style wheels made up (there is nothing off the shelf that will fit) - pretty expensive, and as you surmise, will limit your choice of tyres considerably if you want an off-road tread pattern, especially in far flung places abroad.
I'm not saying don't do it (I did it - rode 18,500 miles in less than nine months on one), but then I wanted a pukka off-road machine first, and was prepared to put up with the on-road compromises so I could enter the odd rally... however, I now have a XT660Z Tenere which is a better travel bike in every respect, and not much worse off road (in trail riding conditions) to be quite honest!
If you're intent on both having the same machine (which is a good idea), then while a DRZ400 may not be quite as glamourous as a 650R, it satisfies the shortcomings I list above, is very competent both on and off tarmac, can be bought cheaply, and is physically not as intimidating for your other half...
Just an idea...