I guess my question boils down to am I understanding the basic elements.
Shape mod: controls how wide the pulse is
Frequency: how fast it triggers
Amount: how....high on the Y scale a pulse reaches(like if looking at an oscilloscope)? I don't really know what this does. It goes +/- 127
Not quite accurate the way you describe it, and therefore your understanding will be off a bit. Try looking at it this way, from a physical point of view:
Shape mod: changes the waveshape. Twist the knob manually to hear the different shapes.
Frequency: how fast you physically twist the knob back and forth around a set point.
Amount: how much you actually physically twist the knob back and forth. Low amount, you barely twist the knob back and forth. Medium amount, you make wider twists back and forth. Max amount you twist the knob all the way counterclockwise then all the way clockwise, and back again, repeating.
So for example, if you set the waveshape knob at noon, you get a certain sound. If you twist the knob to 10 o'clock then to 2 o'clock, and keep going back and forth, this is a medium amount. If you do this slowly, say back and forth slowly over 2 seconds, that is a slow LFO freq. If you twist the knob back and forth quickly going from 10 to 2 o'clock 3 times a second, that's a quicker LFO rate. Hope that clears it up for you. It's really pretty intuitive, and should just "click" when you get it.