Version 1
As you can see, this sump is a 2 chamber system. The baffles are a set of three. Each one should be 1.5" and the middle baffle should be 1.5" as well from the buttom, 2" will be fine to... its up to you, just keep it the same inch throughout the baffles. Do not go from lets say 2" to 1.5" and then 2" again. This would free up and be less restrictive on the water entering the return pump chamber. The water coming from the overflows should be calm by the time it hits the set of baffles.
Microbubbles will almost be eliminated by the time it goes through the set of baffles. The problem with your 2 set of baffles is that after the bubbles go through the 1st baffle it goes down and so the bubbles follow through and the pump automatically takes it back up the return, thus the microbubbles problem.
Also, I put the refugium on the right side because all of your pictures the refugium is on the right hand side, but if you could either place it on the left side of put the return pump chamber on the left side it would look cleaner and be better.
Version 2
Version 2 is like version 1 with the exception that it not has a chamber for the water entering the refugium. The baffle distance would be closer to each other because its less flow going into each chamber.
*** Some important notes:
-Return chamber should be big or a decent size so that it will not run dry accidentally and burn out.
-Less baffles are better, so version one would be better in your case, return chamber and baffles wise.
-With version 1, it would provide more room inbetween the baffles... therefore have more time for the water to travel and be less turbulent once it going into the return chamber.
-I would really advise you to place either the return chamber on the left side or the refugium on the left side so that space will be utilized better. Less piping and so on will be used.
-Also try not to use sponges and so on, it can only cause problems later on.
I'm sure i have more input but I forgot.