With strong storm winds the ship would be set (moved) toward shore more than it would be making headway (traveling in the direction of your course), and hence it was likely that it would end up on the beach (or, worse, on the rocks).
(the ship; would be set more; ) (it; would end up; on the beach (or, worse, on the rocks) (the ship; moved; ) (it; would be making; headway (traveling in the direction of your course))
the ship it the ship it
would be set more would end up moved would be making
on the beach (or, worse, on the rocks
headway (traveling in the direction of your course)