What you've discovered are picking dynamics...which is GREAT!!! The amount of pick attack you use (how hard you strike the strings) is another way that you can add some feel, emotion, etc. to your playing and make it more dynamic - more "professional sounding" as you put it. You'll also find that certain amp settings will respond differently to this. For instance, if you set up a gritty tone where the amp is right at the verge of "breaking up", you can play clean by not digging in to hard with the pick, but once you start digging in, you get a more distorted sound.

Sometimes, that "harsh tone" you describe may be what you want. Once you have control over it, you can bring it out when you think it's appropriate.

Sounds like you are making some awesome progress - good for you!!

One day you should consider making a recording and posting it on the listening post. We'd love to hear some of your playing!!