Shoulders definitely need a little time breaking in with a pack. Sometimes though chafing issues are pack fitment, so you might mess around with that and see if there is an improvement. As the weight goes up, pack fitment becomes more and more important.
Anti-chafe cream can provide some relief too (it's good to have a small tube on hand as shoulders aren't the only thing that can chafe )
I think you're on the right track, build up your aerobic base with shorter, not overly taxing hikes- volume is king to build the base.
