I had a 2001 NX650 Dommie a few years ago and it took me everywhere. From an 800km motorway round trip to Valencia Motogp, Morocco, to spending a whole day following a group of enduros on a cross-country event. The XR 650 would be my choice if I was to build a bike for proper adventure trips. The Dommie is in essence, an air cooled, soft and gay XR but can still kick you in the nuts as well as give you a good time. 
 A few things I would do to an XR though is change the rear wheel or at least the hub to something with a cush drive (XR650L?), and also a bigger oil cooler. I think XR's have a small oil cooler (the early ones anyway) mounted on the headstock but not good enough if you're in a hot climate and giving it some beans. That was the first mod I did on my Dommie as being air cooled and living in a hot climate, in the summer, anymore than a few minutes stuck in traffic and the engine would start sounding like a 5 yr old on a xylophone. It's such a straight forward, easy job to install an oil cooler, I don't know whay Honda didn't do it in the first place. (Yes I do, cost). I still have a hankering for a build the same as what your thinking. In fact, I have a friend who's got an XR (although a 600) ready for me to buy when ever the funds permit. Go for it and post up some pics.
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P.S.
Gratuitous photos of my Dommie enclosed for no other reason than your post made me think about that bike. I regretted selling it ever since.
 A few things I would do to an XR though is change the rear wheel or at least the hub to something with a cush drive (XR650L?), and also a bigger oil cooler. I think XR's have a small oil cooler (the early ones anyway) mounted on the headstock but not good enough if you're in a hot climate and giving it some beans. That was the first mod I did on my Dommie as being air cooled and living in a hot climate, in the summer, anymore than a few minutes stuck in traffic and the engine would start sounding like a 5 yr old on a xylophone. It's such a straight forward, easy job to install an oil cooler, I don't know whay Honda didn't do it in the first place. (Yes I do, cost). I still have a hankering for a build the same as what your thinking. In fact, I have a friend who's got an XR (although a 600) ready for me to buy when ever the funds permit. Go for it and post up some pics.Â
P.S.
Gratuitous photos of my Dommie enclosed for no other reason than your post made me think about that bike. I regretted selling it ever since.