my two cents:
I own a Sport Classic Biposto with upgraded suspension, wheels and brakes, and I also own a 05 999S, though not an R, it's a pretty incredible bike.
If I had to pick one to keep between the two I would be stumped. They are both incredibly different rides and are both amazing for their own reasons.
The 999S is way more comfortable than the classic, and it's my ride of choice for spirited canyon rides. Very nibble, endless straight torque curve, superb engine, well balanced, I can go on. Really a dream to ride. I've owned it for about a year and 1/2 and put 2500 miles on it.
I have owned my classic since 2007 (bought it new) and have put 33K miles filled with multiple-day rides across the southwestern states and in Europe. So it's more than doable with the right suspension, (I have olhins shocks in the back and showa forks from an S4R and a comfort seat), but it's still slightly back breaking.
the DS1000 is a thing of beauty, the power delivery is super smooth and it's plenty quick. However if you're after the "rocketship" feeling, it will tap out eventually. Having said that it's more than anyone could ever need on public roads, it's robust and simple, and requires less maintenance than the more complex testastretta.
My only reticence with taking the 999S on a multi-day ride is the fear that it may not make it without any problems. Not to say that the bike isn't reliable, it's really never given me any issues, but it's more fragile and frankly, not designed for touring. Maybe that's all in my head.
300+ miles a day on the naked classic will test your neck, so you might want to explore a screen option.
For the use you describe I would look for an SC, but basically I think you really need both bikes to be fully happy.
If you're considering a Walt Siegel then you can certainly afford both.