You could take a look at the H14 mast step pin instructions http://www.hobiecat.com/support/pdfs/21380001.pdf
as the early Waves used the later H14 mast base/stepping pin (early H14's did not even use the pin at all, so it was a later retrofit). Yes, the pin should be removed after stepping.
Don't forget to pick up some teflon mast pivot wafers the next time you are at your Hobie dealer. See page 8 of the H14 manual. http://www.hobiecat.com/support/pdfs/e_h14manual.pdf
There are loads of subjects to research on this forum. Also feel free to post new questions, this is a very helpful group!
Congrats on the purchase