First off it was a hard read due to the lack of paragraphs but I got through it. (haha)
As for sump size my general rule of thumb is the biggest possible to fit in the space provided which increases your water volume and makes water chemistry easier to control and maintain.
Personally the chambers depend on a lot of things, I will never have a sump without a Fuge again. That is a personal preference. What are you going to be using in the sump? Reactors? Future internal skimmer? I would plan for that so you don't need to renovate and have the option to upgrade! Your refugium you don't want to have the entire return rate flowing through and should aim for 3-4x your system volume. (You could always bypass T connect your drain plumbing with a ball valve to controll flow through your sump.
The sump will be switched and controlled with an ATO? If not I would tell you to make your return chamber as big as possible or you might be filling it every other day which is a HUGE pain in the A$$.
If you're talking about the space clearance to the top of your sump to be 3.5 inches then that should be okay but I would make sure you plan for power failure and your sump can handle the backflow, also for extra security I would plumb in a one way check valve on your return so in event of a power failure you don't have a huge backflow it would be important to keep it clean and working these have a tendency to fail on some reports. (They're also really expensive)
Your first chamber coming from your tank depends if your using filter socks or just letting it flow into your sump on this chamber I usually only run a under baffle again a preference.
Baffles I would do some research into what you want I've came to the conclusion that an under over is all that needed and that 3rd baffle is just a choice. I have never had a problem with micro bubbles with just using the 2 baffle system
I guess to better help you, or make better suggestions I/we would need a little more information on what you're aiming at achieving in your sump. Also a picture says 1000 words and even a drawn picture on paint or a piece of paper does the trick.
Good Luck
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