If you only paint the outside it won't matter about the paint too much, and will still look black.
As for the silicone, there's some aquarium stuff that's pretty cheap and 100% silicone at some fish stores, forget the name. Pretty cheap is still 3x the price of the clear stuff at Home depot, but $6 instead of $2 isn't the end of the world :P.
You'll want to put your mechanical filter before the fuge, the fuge provides a lot of pods, etc for the tank, and they'll just get caught up in the filter. at the same time, the stuff from the tank benefits the fuge, if possible would you be able to make them in parallel? so that water either gets mech filtered OR goes through the fuge? You'l still get everything filtered and get the full benefits of the refugium.
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