Wow, I'm slacking on keeping this updated, sorry guys.
Fans: two in, one out. Center one is pulling heat out and the two outsides are blowing in.
Skimmer: yes it fits. I did have to build a stand for it out of egg crate. Other than that it works like a champ. The tolerance is very tight between perfect water level and good skimming vs sucking water or hitting the top rear hatch. I actually had to sand the egg crate down a little to get it to the perfect height.
Split return: love it! Although the MJ1200 and MP10 is overkill, the split return did eliminate the dead spot in the front right corner.
I have actually just completed my tank upgrade... already. Only had the BC 29 up for a few months but made a small step up to a Mr. Aqua 48g rimless (no build thread yet, but I completed the tank swap tonight... been a work in progress for some time as I built my own stand and sump.