Too high? Get over it, all bikes are too high for most people. That's just the way it is. Not that it matters, but the height of the KTM500 is one reason that I didn't get one last year.
Handguards and a bash plate are pretty much required. Get those first. If you want to ride the tech trails change the gearing now. My Beta came 15/45 and it was almost impossible to ride the tough stuff. I was able to go 13/48 with my stock chain and that was good for me. With a little wear I was able to go to 14/48 for the desert.
I doubt the smog equipment is much of a negative, but it has been known to fall off. Now do some free suspension setup and ride. Figure out what other stuff you need from actually riding. Your priorities may be different than others.
For example I've seen several posts about getting a pipe. Twenty years ago it was a great suggestion. Today, not nearly as much. Most stock pipes are pretty good and there is not all that much to be gained. There is also the noise law. If the pipe has not been certified to meet noise levels you could get a ticket on the street. It's very unlikely to actually happen though.