New Rider Questions

You need free-play in throttle, brakes and clutch so they aren't always 'engaged', even if not even noticeable. Last thing you want is your throttle or brakes to stick! Make sure to check free-play often on all three of these parts as you break the bike in as they will change a lot during this period until they've settled. I've only ridden mine for 3 days and I already had to adjust clutch free-play! Brake free play I don't believe is adjustable on these bikes(but I could be wrong), so if you ever have a problem, contact the dealer.

And no, nothing unsafe about adjustable levers, just make sure you have them installed properly!

I tend to do all my shifts around 5-7k rpm while I'm breaking the bike in and haven't had any problems with smoothness. Just practice practice practice. Make sure you're above at least 5k though as others have said in another post. Also, don't pull the clutch all the way to the handle, just half way is all you need and you'll get a smoother shift....this is why clutch free-play is important!

If you've never used a clutch in a car you should try it. I think it helps a lot in understanding how they work and what you can get away with. Think of it like this in its simplistic form. For instance, and with the free play in mind, when you start to pull the clutch in, it starts to pull two spinning platers away from each other (like disks). So about half way or so, these 'disks' are no longer in direct contact with each other and the remainder of the pull is just spreading them apart further (not necessary to do). Even in a car you can feel that this 'remainder of pull' is very easy, indicating there is no more friction against the platers. In a car as well as your bike, you can begin to shift gears at this point (also called speed shifting).
When I pull in the clutch I usually just clinch to a half fist and with the shifter preloaded (meaning I'm putting pressure in either direction on the shifter) the shift rods will just fall into place once you've disconnected the platers (just like in a car, it'll just 'pop' out and into the next gear you select).
This is just a simple way of thinking about a clutch and gearbox, and by no means exactly how it works, but I've explained that to fellow newbie stick shift drivers and motorcyclist and it seems to help their understanding without knowing all the real mechanics in play.
Oh and one huge difference between a bike clutch and a car is that on bikes you can't really 'burn' it like you'd do in a car. Different oils in play (oil is really burning, not the clutch itself). So feel free to 'ride the clutch' on a bike. Not forever but a minute won't bother it one bit. That should have been explained to you in MSF class as you'll need this function on your narrow space u-turning technique.

As for the shift points...you have to remember the bike is for sport. They are built for high RPM riding, unlike a car. So between 5 and 11k, this is your 'power-band'. So any maneuvering that needs 'juice' you'll want to be in this range. When I'm canyon riding I'll stay in the 7k and up power-band. Of course you're not saving gas here but when you're riding for speed and pleasure, no one really cares about the $8 it takes to fill her back up. **of course this is after the engine break-in period**. I guess what I'm trying to say here is that if your below the 5k RPM range, the bike has too little gas being fed to it to maintain consistent pressure and that's why the engine breaking is so hard. Therefore, when you shift at these lower points, you can feel the engine drag much greater. To counter the drag, you can keep the clutch 'slipping' a little until it's fully released and not going to give you those big jerks.
Hope this helps a little bit, along with everyone else's input. Happy 4th!!