Could I substitute a boneless pork loin for the pork shoulder?

Merrill's right--loin is a pretty lean cut, while shoulder (also called "butt" confusingly) is very fatty, which is why it's often used for slow-cooked pulled pork. I would stick with shoulder for recipes with a long cooking time like this one.

I don't recommend pork loin, as it will dry out and become tough -- you want to use a less lean cut that will soften as it cooks.