Agree on collapsing MX and MS per physical site into the same combined network.
Meraki recommends putting wireless into the same combined network for that physical location, due to some of the RF math they crunch behind the scenes. That's what my company has gone for. We push SSID changes thru the wonders of API.
For moving your switches, keep in mind that they'll lose most settings. It's pretty easy to copy over basic switchport configs. I make no promises here but I used this script when I had to move L2 switches around. (Busy or I'd add better comments... sorry!) I remember it working fairly painlessly.
You could grab the idea I used and make it into something that'll do more than one switch at a go. I was only moving four or five switches, so I didn't bother at the time.
L3 interfaces, you'll have to recreate. But if these are stores, I'd be willing to bet you haven't got L3 switches everywhere.