How long are you planning on living in the home?

If it just a few years, as compared to someone who is 40 and planning on staying for rest of life, that can change your plans.

given the wild weather were getting I would go with the waterproof membrame over the entire roof, just or safetys sake.

definetly get the chimney with loose bricks rebuilt, with a new chimney mortar cap.... otherwise rain can get between the liner and bricks and when it freezes break the liner and have it fall in and block the flue.

you dont want any loose bricks hitting your nice new shinglers in a storm...