Well, today is the 2 week anniversary for the tank so I have a few thoughts and I'll also share some of the thoughts others have had.
First, penductors are well worth it, including the additional price for a pressure pump. The flow is totally amazing and I feel like I could run the whole 6 foot tank with just the Mak 4 penductor closed loop flow if it was just for softies. The gyre baffles don't go all the way to the front of the tank (1.5" shy) and the amount of bleedthrough from the 2 sides of the baffle plates is considerable. I did consider this but didn't think the effect would be so dramatic. I'll be extending the baffle right to the front once the swap corals are out and I have some more room to move things.
On a general note, there has been little apparent recycling of the system which I attribute to well cycled, robust live rock, large, frequent water changes during the initial 2 weeks, and the enhanced flow which I think makes for a higher DO level overall. From day one, I've had better pe in this system than expected and a lot of the corals are showing significant growth in just 2 weeks.
Conclusions at this point-
"Linear" flow is no problem in reef tanks and in reality becomes turbulent flow right around the animals anyway.
Reinforcing flow patterns with all outlets and returns in the tank is good.
Penductors are very cool.
Gyres are also very cool but need to be done correctly.