If you have access to a good butcher, they can probably order a skin-on shoulder for you. Of course not everyone has that option, but it's definitely worth asking for if you can.
There's probably no substitution; the skinless version simply will be absent of the cracklings texture on the outside.
As for the recipe alternation, it is likely that the cooking time would be reduced. In any case, your goal is to reach the same internal temperature (170-180 degrees).
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As for the recipe alternation, it is likely that the cooking time would be reduced. In any case, your goal is to reach the same internal temperature (170-180 degrees).