The deckhouse on Naseby in the van de Velde drawing resembles the arrangement on the Sheldon model, which includes a cockpit or lowered deck section abaft the house.
Most ships of this period, (including Vasa) have at least one gundeck port on each side which points directly forward. On Vasa, this is the first port on the lower deck. Often, this carried an especially heavy or long gun, (as on Vasa).
I am not sure how to respond to your quesiton about the bow shaping. The form of the Sheldon model looks to be similar to other ships of the newer type produced in the 1650s, after the model of Speaker, and so is relatively sharp, with some hollow in the lower part. I expect that Naseby and Äpplet would both be very different in hull form from SoS.
Recent research suggests that the model we have is likely connected to the construction of Riksäpplet. Niklas Eriksson has recently published a book (Riksäpplet: Arkeologiska perspektiv på ett bortglömt regalskepp; Nordic Academic Press 2017) which discusses the model and investigates this connection quite closely. Analysis of the hull form of the model suggests it should sail fine on the design waterline. It was made by a professional ship designer, so it is not a "toy", but embodies his ideas of how a large warship should be configured. The ship built from it had no problems as a sailing vessel, and was only lost through poor management in an anchorage.
We are working on a detailed documentation of the model, but do not have a definitive timetable for publication.
It looks like this grating is directly above the hawsehole, so it would allow the jeer capstan on the upper deck to be used in assisting to raise an anchor. This is one of the uses for the jeer capstan attested in 17th-century sources, such as Smith and Mainwaring, but it requires a lead for the tackle, which this hatch provides. It also looks like there may be a double block already mounted in the right place, or perhaps a whole tackle, so one would only have to lead the fall up through the hatch to the capstan when needed. On Vasa, there is a suitable gap in the grating rather than a removable section.
Indeed! Because Vasa waited so long for its main armament (the 24-pounders), they were really scraping the bottom of the barrel for the upper deck guns, amassing a motley collection of antiques and obsolete types.
The problem is that the decks do not survive on wrecks, for the most part, so we do not know. On Vasa, the binding strakes run the length of the deck,although sometimes with some odd joinery towards the ends. One of their functions is to frame the hatches, but they also contribute significantly to the longitudinal strength and stiffness of the hull, thanks to complex joinery and bolting through the beams.
I tend to use Humbrol enamels for painting small details. Their formulation has changed over the years (not as good coverage as there used to be), but they are reliable, there is a good selection of colors and they are widely available. If they do not have a psecific color, you can often mix what you need. The poxy little tins are a pain, and it becomes difficult to seal them after a while, but you can take some measures to prolong the life of a tin (stir the paint to mix it rather than shaking, clean the rims and and lids, etc.).
Other brands I have used successfully in the past include Floquil (their railroad colors offered a bunch of good options for ship modellers) and Model Master, although the latter are geared very much to aircraft and armour modellers.
If you do not want to use enamels, I like the acrylics in the Gunze Sangyo Mr. Color range. Very easy to use, good coverage, no smell or fumes. Wide range of colors, but aimed at the modern military modeller.
I do not use oil paints for the most part, as the drying time is quite long and the surface is too glossy for me.
Outboard ends of ringbolts for the gun breechings and tackles were hemispherical heads about 50-60 mm in diameter, as far as we can tell from impressions in the wood and rust clumps at some bolt locations. No rings, no forelocks, no split pins (we have no evidence of split pins anywhere in the ship, it is a later technology - forelocks were the 17th-century equivalent).
The windlass is removable (it was found inside the ship, in fact)and mounts in a pair of brackets nailed to the inner face of the framing. See the attached photo and reconstruction drawings, which should make the arrangement clear.
I am afraid that the contracts will not tell you as much as you would like to know. They only specify the number and length of anchor cables to be carried, nothing about the anchors themselves. I have a specific contract for the ship Tre Kronor of 1626 which indicates the weight of the anchor cables, but otherwise the Swedish records are not very detailed on this score. English inventories and specification books of the 17th century are much more detailed by comparison.