Alright, just looked at your pictures closer and saw a few things that answered some questions. I was thinking you manifolds were exhausting the water but just internal circulation. Thats good but still think you going to run into heat problems with the up pipes unless you can find a cooling system for them as well. Then you have to have an intercooler setup. That will take up room and have zero air circulation unless you can find a heat exchanging coil setup. that will take more plumning etc.
I see the EGR is off and i'd leave that off and bypass... POS in my opinion. I'm very intrested in the project. Please keep us posted. I'm very familiar with the LMM and always looking at ways to improve performance.