[Edit: I have written on, moodle theme modification which we did at http://www.iank.it/category/e-learning/
for http://www.edupristine.com/ca ]
It will be very tiresome to create a complete new frontend for moodle, I would suggest choose a theme which looks closest to what you want and then start modifying it.
You will have to understand moodle's database and tables structure and also Moodle database Manipulation API.
After this you can straight jump into tinkering the moodle code and understand its core functions wherever required.
You would also benefit from many plugins available if you modify the moodle frontend instead of creating one.
