Before I post the final results on the Viribus Unitis, here's a list of things that could and should be improved.
The must-have tools I've posted about before did really come in handy: a pin vice and tweezers are very basic and cheap things that really improve a modeler's experience.
Prepping the wood, sanding it multiple times and painting in thin layers will result in very nice surfaces (that can still be ruined a bit by torpedo nets).
Painting in sub-assemblies is great for getting paint where you really need it, and not getting it to places where it's not.
It's kind of difficult to get the right material for cannon barrels, I'll try and remedy this by using 2mm thick brass tubes sanded to a tapering shape (might still be easier to sand than toothpicks). The other version is to use bakeable plastic with a strengthening rod inside.
While paper clips are OK for the 1mm and above grade for various on-board equipment and gun barrels, below 1mm more stuff is required. Broom bristles are of a surprisingly similar diameter, so I purchased some 0.5mm steel rod.
Thin layers of air-drying clay will bubble up when painted, this is most likely caused by bad adhesion to the plasticard sheet, and can be improved by prepping the sheet or switching to milliput, which I most likely would have done anyway.
Ship crews are quite easy to do, so I shall be focusing on them more, maybe even pre-paint a large bunch to have them ready when the ship gets done.
Boats should be painted in more detail, or have more sculpted detail. Perhaps I'll make boats from bakeable sculpting clay.
My next project will be USS Wyoming, a much larger ship than the Viribus Unitis, so there's more material cost and prep work involved. The thing I sort of don't look forward to is the lattice mast by the way. I could not even find any proper method for forming one online.