I like the design but I would find a way to make to easy to access your pumps for repairs and maintenance. You can always use hardscaping materials to hide them and the egg crate.
You are absolutely correct. That would be one of the biggest challenges of this, IMO. I would have to size the opening appropriately to allow my fat arms to access it. haha. That, or maybe make one end of the "floor" baffle movable. hmm..
It seems like the pump on the right is pumping directly into the right side tank wall and I'm not sure you'd get the directional flow that you were looking for. Maybe consider the pump on the right being outside the baffle, pumping the water to the left, but hidden by rocks and such. Get flow like this:
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For sure, that's not a good spot. In my mind, I anticipated having a higher pressure there because it would be trying to lift the water, so building pressure would be the name of the game, but you are right, that needs to be rethought. Actually, it might be the perfect use for one of these (or something like it that looks like it belongs in freshwater), pointing the pumps back the other direction like you indicated on top of the egg crate on that side:
http://www.bulkreefs...k-6200-250.html
I've never tried anything like this but have thought about it a lot. I have a 75g tank, so not really a lot of room to work with something like this. I decided instead to go with a strong powerhead to achieve flow from the left to right of my tank. I'm hiding it within and artificial root structure. I'll definitely be following your build though. It will be interesting to see what you come up with. Good luck!
Thanks, I appreciate it! And the input! 
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