I think you're gradually getting the hang of NL. You've got the right idea, it's just the exceution that needs a bit of work. I'll break it down a bit:
1. Lift Hills - You've got the right idea with having it in three sections. I think you just need to tighten up the radii on the entrance and exit pieces. They're a bit too open.
2. Segments - Up to a point, more segments means better track. It allows you to control the shaping of the track much better and can help prevent bumps and jerks. I generally use one segment to get the rough shape of the section I want, then use the 'split' tool to break it down and get more control over specific areas of the section.
3. Smoothing - Truth be told, most of the transitions were pretty jerky. You've got two options to try and fix this. Firstly you can use the simple Ctrl+G method when you've got one (or a few adjacent) segment(s) selected. This works better with more segments and the track won't distort too much and will keep the shape you want whilst also smoothing out the transitions. The other option is the so-called 'I-smooth' method. For this you select each segment in turn and press 'I' to straighten the segment. You then work through a bit of the ride segment by segment doing this. At first it'll completely **** the whole thing up, but then if you select all the pieces and press Ctrl+G then you end up with a pretty smooth section of track.
4. Banking - There's an easy way, and a hard way (well, not hard, but in comparison) and a way that's kinda in between. The easy way is to simply guess. Look at the bit of track, think about the speed of the train, the direction its travelling and the forces on the riders and just bank the track until it looks right. You'd be surprised how close you'll get by using a bit of sense.
The hard way is to sit down with a pen and paper and work out the bankings. This seems like hard work and I think you might as well just use Newton or AHG if that's how you want to build. The way in between is to guess, then ride in the simulator and correct. It's fairly quick and should get you pretty close.
I've taken your track and had a bit of a play (I hope you don't mind!) to show you what can be done in a short space of time. All these changes can't have taken more than about 10 mins.
-Cleared supports
-Used the I-smooth method to get most of the transitions looking a bit better
-Went round and corrected some of the banking issues
-Had a bit of a play with the shape of the entrance to the brake run
-Re-applied the auto-supports.
Now I'm not claiming that this is the best I could've done. I'm sure given longer I could've sorted a few more of the pumping issues out, but it shows what can be done:
http://www.mediafire.com/?jtue7dudsx5thpy
Hope this gives you some pointers, and sorry to seem like I'm taking the whole thing apart. Like I said, you've the right idea, but just needs some practice.