I'll cut off the the top, re drill, re glue. Not to much drama. At least I didn't start laying the fiberglass yet
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I would leave the top off for as much the sealing and fiberglassing as possible. I know eventually you want to overlap the fiberglass up on the top but I"d leave that for the end of the process.
I have maintained several tanks 36" or taller. I was younger then and as much as I loved them, they were a pain. I do agree with most of what others have said about the advantages of decreasing height and increasing the front to back depth if you can. So many advantages for a first time DIY build.
One thing I don't agree with is that eventually the fiberglass will crack. With enough layers in theory you could build a tall tank out of nothing but fiberglass. But do understand that the less you rely on wood framing and the more you rely on fiberglass reinforcement, the more the tank will cost.
If you're already planning on marine resins, why do you also want to use a paint over it? You can just tint your final layers of resin.
If you do use the paint, make sure you install your window first or at least make sure whatever you use to attach the window (silicone or whatever) bonds well to the paint.
My big issue with using paints is that they make furture repair difficult if the resins you used to seal the tank in the first place don't stick to it. I did a quick google search and it seems Zophar is tar based? If so I would not expect epoxy or polyester resin to stick to it nor silicone, at least not well.
I don't have a problem with using two different types of sealants on a plywood tank. But it it were me I'd using it as a means of sealing a hard to find pin hole leack or a leak that sprung up in the future.