I'd consider adding some loaches and pleco's. With that size tank you could easily add some of the larger species as well. Aside from that, I really like that stocking list. It will be a site to see.
Ya might considering adding a small group of a larger schooling fish, to give a bit of variety and contrast to the larger schools of small fish.
More filtration is always better. It may just be me, but I would not see a problem using your old hook ups from when this was a reef tank.
I don't think your fish will have a problem with the flow, especially in such a large tank. They will just cruse around having a good time. I tend to think the best way to install filters is to have them pull 'dirty' water from the bottom of one side of the tank and dump the 'clean' water at the top of the opposite side of the tank. Granted, this may not fit in with the plumbing you already have, but I don't think it is worth the time, effort, and further mutilation of that tank to move the pipes.
Use the hook-ups that you have, it should work out fine.
Thats gonna be lots of plants. You may want to go in and build some structure (rocks caves and whatnot) so you can have some plants in all the vertical levels of the tank. There are some plants that would get tall enough, but I think having them grow to that height wouldn't look as good as giving them something higher in the water column to grow on.
Maybe some rock caves with 'plateaus' where you can put some substrate and plants? I think that would look pretty wicked.
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