Last week I asked Eddie about making a mod to the sump to combat the reported micro bubble issues, and he said it's not the sump design but the skimmer he used to ship as stock. I'm assuming that meant before the Bubble Magnus. It looks like you're having micro bubbles with the BM, though. I ordered my 39G without the BM skimmer and am looking to buy one. Will probably go Tunze unless anyone has better suggestions. You pay a premium with Tunze but I've always been happy with the results.
I believe that the micro bubbles get back to the tank because the sump is so small. both the drain line and skimmer create the bubbles and there just isn't enough room for them to dissipate before getting to the return section. I know I keep going back to my old 120 and how it didn't have bubbles but I think that one the sump was designed better and two the sump was big, 45 gallons, so there was lots of space and time for the bubbles to dissipate before getting to the return section.
If I were to do this all over again from the beginning I would not use the "stock" stand, sump or lights. The stand is well built but doesn't provide enough space under the tank. I would put the tank on something that allowed for at least a 24" sump plus room for ATO and other storage.
The sump is just too small to combat the bubble problem and still have decent flow.
The light is actually OK except for the fan, which sounds like a plane is landing in the living room, well not quite but it is unacceptably loud.
So far the mods I have made have been
1)add an exhaust fan to the cabinet, with out it I have a small sauna under the tank.
2)replace the fan in the light with 2 17 db computer fan that moves 75cfm. I get no heat transfer from the light to the tank with these fans going.
3)modified the sump to get better water levels, flow and help with the micro-bubble.
4)added a filter sock to the drain line

- not sure why I am so adverse to filter socks but I am.
5)Set up a small ATO that sits on top of the sump. The container only holds about 2.5 gallons and I have to fill it every two days but at least the water level is kept constant an I don't have large additions of fresh water daily.
I still get a few micro-bubbles in the display tank, maybe a couple dozen or so. They are definitely coming from the BM skimmer which sits in about 8.5" of water. Incidentally the BM website says to put the skimmer in 8"-10".
I can live with the few bubbles since I can't remember ever scuba diving in a perfectly clear ocean.
Future mods will be to change the lights out to an LED fixture and to build a new stand that will house the electrical in a separate compartment on one side and have enough room for a 24" sump, larger ATO, dosing stuff and storage.
As far as the skimmer goes if I was going to get a different one for this sump it would be the Tunze as well. Not only does Tunze make a good product it is one of the few skimmers that will fit easily.