My thoughts are:
I think it is AWESOME that you took the initiative to learn. When I first started with blender, the senior members (whom I respect and trust) would say that customizing the blender interface is really easy and after doing some research I agree.
As far as the progress you have made I believe it is a matter of what works best for YOU. I mainly study modeling and animation so my customizations have to do with that.
Keep learning to customize and ultimately what works for you is what is most important. What works for me or anyone else for that matter depends on the person and what as well as how they use blender.
It is not normally recommended that you waste any of your valuable time trying to learn what works good for someone else because everyone has their own individual workflow as well as uses for blender.
If you can customize the interface in a way that makes your life easy than by all means do it.
I have found that customizing the inteface doesn’t interfere with the overall performance and functionality of the program. The interface is only a GUI meant to serve the functions that are currently available.
Customizing the interface is one of the many advantages of Blender especially because it is open source. Most proprietary programs such as Maya can only allow you a limited amount of customization because the source is not available to the public so you might as well take full advantage of this unique feature that Blender has to offer.