Planx, what kind of terrain will you be riding on and what kinds of roads (and road speeds) will be involved? We can help narrow things down a bit.

Well, keep in mind that while these bikes are pretty capable off-road, they are not full moto bikes.  Depending on how hard you're riding, these bikes are not ideal for sick MX and jumps.  You need to consider a proper MX bike for that.  It'll get you around a track at a moderate pace and it will eat up those trails, roots and all.

MX bikes are best for MX jumps, but the most capable dual-sport out there for this would be the WR but it will be hard to want to take to any speed over 60mph, though it can go well beyond that. It's a tall bike but it has 9" or more of travel. I ran that thing over a dry creek rut without even feeling it. It soaked it up so nicely. It was just 1.5" too tall for me.

Well... if I were in your situation, I'd prioritize things my way. So don't follow me on this because it will irritate you. Anyway, to me, the jumps take a back seat to everything else. So I'd look at something that can get me to school and I also ride year-round so I'd forsake some top speed for something that works well in cold. That would put me on a TW200. It's ugly and I'd never take it up to 60mph but it's probably the best winter bike there is and is awesome on trails... especially soggy stuff as long as it isn't caking a few inches of mud on the tires.

If I were you, I'd look the CRF250L. It's not as tall as the WR so it's already better stock. But if the geometry can be maintained with a 1" lowering kit then I'd look very seriously at that option because this bike might be THE ONE for what you've described. It's light enough to throw around on the MX track a bit (not like a bike that's 70 lbs. lighter but still fun) and it has lots of suspension travel. It is also fuel injected so the winter startup is great.

It would be great if you could get something used but I'm not coming up with anything that can tick all the boxes. Anybody else wanna chime in here?

Update to my Dually progress. Just went to Yamaha today to sit on the WR250r again, but unfortunately they sold out of the 2013 WR250r models. But in good news, the "even higher" seat height WR250F was there and for some reason, I found it to be a little comfortable. Two feet down was still quite difficult, but with one foot down, it wasn't that bad, well not as bad as I remember with the previous WR250R I sat on... Maybe it was lowered slightly and maybe the suspension was quite soft. Either way, I'm certainly going to wait for the 2014 models to come in and see how that feels with 0.6 inches lowered. If I need more, I will look into the Yamalink that drops 1-2 inches from what I'm told.