Oh, sorry to hear that. I hope the damage was all to the machinery?
You bought the bike without asking?
"We"?
That all sounds very sensible (apart from planning the tour before asking her).
For two on a tour you'll need more than just a top box unless you're planning on using the credit cards a lot. I like a tank bag, consider throwover panniers or something like that too. Make very sure that the luggage will stay on the bike, some of the weight ratings for bike luggage are ridiculously low, like 4.5kg for my Givi panniers.
Keep the chain oiled. If I'm riding a bike with chain drive I always take a little contact lens solution bottle with oil in it. In bad weather you might need to oil the chain every hundred miles. A centre stand makes a huge difference to how easy it is to oil the chain and perhaps to how often you get around to doing it. For touring I'd have gone for the 900 (shaft drive!) but the 600 will see you all right and you can't grumble for four hundred quid. Make sure everything is kept well maintained and build up the distances gradually. If you don't have it serviced by the book, at least make sure the engine oil is changed regularly and the control cables etc. are kept lubricated. Keep a kit list. Keep a log. Make sure the engine isn't burning oil. European breakdown cover is worth considering but you might not get it depending on the age of the bike. Check the regulations for driving a bike in the European countries you plan to tour, for example in some countries back protection, a first aid kit and spares for all bulbs are all legal requirements. You probably won't be allowed to do silly distances daily if you're with SWMBO, but take care not to get over tired. I like to stop and make a brew if I start to feel tired, my brew kit is usually handy in the tank bag.
Have fun.
http://www.jubileegroup.co.uk/JOS/misc/dscf2036.jpg
http://www.jubileegroup.co.uk/JOS/misc/dscf2153.jpg
Oh, and make sure you can get where you're going on the tread that's left on your tyres.