Will we have the ability to set perms for our shops, like in regular factions?
Yes to F access. You may not claim or invite (staff will handle members). Inactivity timeout is currently 10 months. That's not policy, just a random setting for now.
Could enchanted items and shops for those items be a problem when doing the move?
If so could it be possible to set the shops after the move, I could probably do it within a day or two?
Enchanted and any #id shops should work mostly fine from Build4, currently existing shops only. Shops from other worlds and some new shops made after march 24 will need to be remade. The /itemid id's are sadly world unique, but we imported Build4's id database.
Moving banners and chest contents works fine. Even animals and item frames usually work, most of the time.
Armorstandpets are available on Shop world.