Just a couple of quick tips off the top of my head (I have't dug into your model too deep yet) - it looks like you're getting the hang of it!

After you create a surface from some curves, you probably should hide the curves, or possibly save them off to another file and delete them. The reason why is that curves have a priority in selection over surfaces (since otherwise they would be very difficult to select if you could only select them by clicking exactly on them). This means that for stuff like fillets, it is pretty easy to accidentally select one of your old input curves instead of a surface edge, which will produce a different result. This was probably a confusing issue.

Another thing is that sometimes it is good to work in surfaces, and then sometimes it is good to join surfaces together into solids and then do operations on joined edges.

If you are in a detailed area that where you are having difficulty, then that is generally where you will want to revert to separate surfaces. This is one area of flexibility that is nice in a NURBS modeler as compared to a solid modeler like SolidWorks/Inventor - in a NURBS modeler you can work on one surface at a time and join them together into a solid later on.

On the other hand, you will find that solid modelers like SolidWorks and Inventor have stronger automatic operations in several areas, especially filleting and shelling - they will be able to calculate a lot of types of fillets that MoI will fail on. But when they fail you are kind of out of luck...

Anyway that's just some generic advice and thoughts, I'll still take a look at your specific thing here.

- Michael