Protein skimmer?
I would put shutoff valves between the refugium and the display so you can dial in how you want your flow. You may even wish to do both. I would...you could find that flow rates were much faster than anticipated, allowing you to adjust to desired rate.
On the tank connections...If your PVC is 2+" (or as large as you can get, larger=better) you shouldn't have a problem with that. Again, a glass shop would be able to cut a hole that size. I would have bulkheads in hand before I cut the hole though so you can insure proper fit.
Return pump=overflow rate(generally, some variables can throw this off.) so if you properly gauge the supply to the refugium, you shouldn't need to back off on the return.
The way you have this designed the refugium fill rate MUST be slower than the other tank. There is no way around this other than say a minimum 3" PVC tank connector. In which case you would need to put the valve on the other side.
This all depends on the flow rate you want in your refugium.