Lots of info there! So here is a long response back.
First, I would never use a check valve on a reef tank. Here's why: they will not properly seat when needed because growth in the lines will occur regardless of whether they have light or not. Sponges will eventually grown in them, bacterial mats will form, its inevitable and a check valve will not perform when needed.
I'm unclear why you have a check valve? A check valve is often used to prevent unwanted flow from the display tank into the sump when the power is off or the pump is shut off. This is a bandaid to prevent floods and dropping the water level too low in the display tank due to back feeding into the sump. Typically I see people try to use check valves on return lines because they haven't designed the system correctly. A correctly designed system should have an air gap/siphon break so that when the power goes off a siphon does not form that overflows your sump. Also some water siphoning back to the sump is unavoidable so there needs to be enough freeboard in the sump to accommodate it. I would argue this is the most important design parameter of a sump. Water on the floor is dangerous, and also can result in problems with your reef since when the power is restored, the pump could be running dry or an auto top off will kick on and lower the salinity of the tank by the amount of water on the floor.
Mike, were you at the swap helping me when we had the flood last weekend? That was caused because the power shut off on one of the vendors tanks and he didn't have a proper siphon break and it overflowed his sump (which was a 5 gallon pail). I think if you search for siphon break here on CR, you will find more info on how to achieve a siphon break.
As far as valving, I would never put a ball valve on the drain line. Valves are a restriction in the line even when they are open and could potentially plug if a fish or whatever flows into the pipe. A plugged drainline will result in a flood and possibly jeopardize your reef. The drain line should be a straight shot into the sump.
Flow rate should be controlled via the discharge side of the pump. I would put a tee on the discharge side of the pump with a valve on it to bleed any excess flow back into the sump. You might find that with new pumps and plumbing that you need more water throw this line than when the pump and piping are older. So its nice to have the valve so you can adjust over time.
As far as sizing of your return pump and sump, the controlling factor sounds like it is the overflow box. Flow through sumps are typically 5 times the volume of your display per hour. So for a 90 gallon, you should be looking at a flow rate of 450 gallons per hour. Also this should roughly match your skimmer's flow rate...so you are in the right ball park for sizing. I would say you have the right equipment for your sump and flow.
Keep in mind, the flow through your return line only makes up part of the flow required for a reef. Typically, 10-30 times an hour total flow in your reef is what you will want to keep everything happy. This is achieved with powerheads or closed loops.
Also I would avoid drilling your sump for external pump and try to keep your skimmer in sump if you can as well. That's mostly a personal preference, but I think having them all contained is safer and less likely to leak outside of the tank. For me, the number one design factor for a reef aquarium is that it doesn't leak or flood.