LMM harness and ECM since I designed a NMEA gateway based off that setup.
http://www.duramaxdiesels.com/forum/showthread.php?t=68389
Still trying decide about using a MAF with the twin symmetrical turbo's. I like the cleaner exhaust at lower RPM the MAF allows, but would either have to run them into a single intake tube or run twin MAF's and build a splitter box to calculate total air flow.
On transmission, the Allison is overkill in a boat. 2-3 and 6th are not used on my buddies. It shifts 1,2,3,4 is under a second, then hunts between 4-5 most of the time and slips in 6th which limps a stage 5 build.... So that's locked out. The two speeds like the COAN are electronically shifted by a button on the dash. One click and both shift from low to high gear, then hold wherever you put them till you push the button again. That's about all you need in a boat is one gear to get on plain and light the turbos, then shift into high and stay there till you come to a stop.
For cooling, the Banks intakes use a cupronickel core that salt water doesn't effect like aluminum. Main difference is the heat transfer rate is better on copper. I would still use aluminum if had too and just flush them out with salt away when done boating. The oil coolers are massive and have a copper core, along with engine heat exchangers. Getting enough water pumping to cool all that is the issue.
Exhaust is all 316 stainless steel tube in tube. Below is set I built for the 6spd boat this spring. Will use similar design with different up pipes to T4 flanges. Likely use divided scroll housing turbos with spool valves to help get them spinning.