Uneven/big gap between door and stop trim weatherstip will not seal
Yes typically you set the stop to the door. Before you do though check that the door is resting even with the outside of the jamb. If it's not, insert some thin cardboard shims behind the hinges in such a way that it "twists" how the door hangs and/or adjust the strike plate to correct that issue before resetting the stop. Remember to leave enough room for your weather strip. Cheers!