Here's my short summary of how to resolve all of these questions:

1. Free will is incoherent because it would violate Occam's Razor, because you have to posit unlimited axioms (one for each person who will ever exist).

2. Morality is also incoherent because it implies some privileged universal sentient perspective (i.e. god) to serve as judge of what's good or bad - and any claims about god are indefensible.

3. We can nevertheless use systems of punishment / reward / shame / honor to guide people into behaving in ways that are desirable to ourselves.

The place where I think Sam loses the thread is in believing in morality.