I did the same thing, design looks great. I would keep the last baffle as is so that you can drain all other sections and leave the media submerged for extended maintenance. It also keeps evaporation from leaving your media exposed, not that it is likely with the water change schedule of discuss. The isolation is a 'meh' idea in my eyes. Keeping a running hospital/quarantine is likely better and easy, but it won't hurt to have it.
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