Everything brown in there, if it's made of metal, has to come out. Anything less than that and you're not doing a responsible job of it.
I don't like what looks like putty up around the fitting at the top right of this photo. I can't think of any reason a properly-installed fitting has to be done that way.
Is the tank the thing at the top? I can't orient myself to see this photo properly.
Don't be afraid to cut a new access hole in the top of the berth. Make it as large as you like; make the corners well-rounded (at least 1-1/2" radius). Use plain pine 1x2s from Lowe's to make a framework of cleats for the opening, situated half under the hole and half under the remaining plywood to be screwed in. I saturated mine with WEST epoxy and mounted them with the same and with #8 screws through the top. If you are tidy about cutting the bunktop out, you can use the cutout for the access panel. (This typically requires that you 'lean in' with the jigsaw blade, something of an acquired, moderate-to-advanced-level skill. If you're up for it, this will ensure you a clean cut and a nice reusable cutout. If not, drill a 5/16" hole, just big enough to insert the blade, in each corner and use the jigsaw for straight lines between the holes.)
I rebuilt most of my bunktop access holes and wrote about it in my blog, somewhere.
I would include in any tank some 6" or 8" screw-out deck plate like the Sea Dog Line ones at Defender. If you can't get your arm and a scrubbing-brush in through the hole, it's worthless.
Whatever the metal is-- brass? --iron? --it should be replaced with either bronze (expensive) or Marelon (slightly less expensive) or even PVC (cheap, good for fresh water, but less durable). PVC is easy to work with, so long as you get good glue adhesion. It dries fast and is easily removable (use a hacksaw) and replaceable (because it's cheap). That gate valve is a no-no for anything. Even a cheap brass lever valve would be better. I would default to plastic for fresh water-- there are many options available now, such as the blue-and-red Whale tubing and the compatible fittings, and their cheaper copycats.
Don't be afraid of installing fittings in water tanks with 5200. It doesn't leak and, from when it's first skinned-over, doesn't leach into the supply. To skin it over quickly, dip your finger tip in a cup of clean fresh water and smooth the bead. A fingertip's radius is just about perfect for any application and this will help the 5200 set up. Best of all, the 5200 will behave in the tank the same way it behaves on your water-wet finger: it won't come off (won't even be sticky). No silicone or bathtub/swimming-pool caulk will work as well.
From the look of it you need to start with some Simple Green and elbow grease!