Question 1:

When using an inner stem, should I plane all the end boards down flat to the apex of the inner stem or try to shape it into a rough point?
Are you using an external stem as well? If so, you can plane of whatever amount suits you. How much you plane off is determined by how thick you plan to make the external stem.

Question 2:

With an inner stem, the hull shear line finishes leaving part of the inner stem wrapped around the stem form piece. Should I carefully saw this piece off and save it for when the deck starts? It doesn't seem like it would be too easy to remove otherwise.
What design is the kayak? I can't picture the problem you seem to be describing unless you mean the stem curves back at the top like a lot of canoes do.
Question 3:

I assume sand the hull, glass the hull then remove from forms, right?
Not necessarily. A lot of people, including me strip the deck as well before starting glassing.
Thanks in advance,

Phil