First off let me say, I don't have first hand knowledge of fuges. I have been researching those to find out the benefits and how they work best.
Many say that the impellor on the return pump chop up the organisms that the fuge produces. That being said most people mount the fuge above the main tank and pump the water up to it while the output of the fuge is gravity driven. - Just something to think about I know you have a few tanks sitting around.
I'm having a little problem with following the flow of you sump setup.
I know the water from the tank comes in from the left-hand side but are you using the return from the skimmer to fill the fuge and the "heater" area - or does the water overflow into these areas? (or both?)
Because if it is just the skimmer return flowing into these areas then you may have a problem with getting enough water thru to the return pump.
Also with the sump being 40" long I don't think you will need that many baffles by the return pump. That length works to your advantage so I wouldn't think that bubbles will get to the return pump. Just IMHO