No, the structure is quite sound. The counter has been reinforced by the inner planking. You can remove the inner support structure once the shell of the hull is created. However, one has to be careful to remove only those supports from the kit that will be replaced by other structures. The hull as it is now is a thin shell, prone to distortion from changes in moisture and holds its ship because of the frames provided by the kit. As the decks are completed from the bottom up, the kit's frames are being removed in sections and replace by the inner planking of the bulwarks and the hull sides anchored by the deck beams.
There are times when, faced with a problem in making a kit accurate, that you have to be fearless in your decision to modify a ship model, after long careful consideration of the effects of that change on later steps in the build. I am at one such crossroad. In order to build the Sovereign in the form that she was initially built in 1635 with the guns closer to the water, I have to undo the features of this kit that were influenced by the form of the ship after 1660.
As I was looking at the deck height and gun port placement relative to the stern, it became apparent that the lower deck is a bit too high such that the stern chase guns would be located too high relative to the gun ports on the counter. This is because the of the kit's design as to the location of the lower deck. It may be possible to raise the counter up 5mm, and adjust all gun ports and decorations to come later. The entire stern will have to be re-evaluated. I think I can squeeze in the lower deck stern chasers with slightly lower gun carriages, but the middle gun deck gun port as drawn on the side of the hull are about 12mm too high as drawn, and the location of the middle gun deck and its ports will be adjusted to match the stern. The curve of the counter needs to be adjusted, so the top planks of that curve will have to be removed and replaced higher on the stern. All these changes came with a close study of the Willem van de Velde and Payne drawings and prints. Knowing that the van de Velde depicted the guns of the lower deck at the newer, high positions in his drawing resulting from the deck being raised in 1660, but mistakenly drew the two ports under the side galleries in their lower, original positions prior to 1660, when in fact they were eliminated, it is logical to assume that the reason DeAgostini designed the gun decks at their heights in the kit is because they copied the deck positions from the later rebuild of the Sovereign, not at the original, lower positions shown on Payne's print. The reason the gun decks were raised were obviously to raise the guns above the waterline to make the ship more seaworthy and such that it would not suffer the same fate as the Wasa. King Charles I had already ordered that the ship be loaded with more cannon that she had been designed for, and to make up for problems of that decision, many changes to the internal structure were made in 1659-60 to get more use out of the ship, including lightening of ship to reduce its draft by removing many of the heavy decorations prior to re-christening the ship
HMS Royal Sovereign. With some tweaking, I may yet be able to align the level of the lower and middle gun ports from the sides to the stern, but without totally gutting and repositioning the lower gun deck, it will be difficult, and the proportions of the stern decorations as shown in the Lely Portrait of Peter Pett may not be successfully preserved. Uwe's solution was to change the shape of the counter and raise the upper transom, judging from his model photographs. It has become obvious that my build will have to follow a similar path. However, despite his changes, it does not appear that Uwe's counter will terminate as high on the stern as it appears in my sources. As a result, I think he may run into trouble with the placement of the middle deck stern chase guns.
Uwe's ship plan with interior decks shown in red
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The proposed redesigned profile of the counter, bringing the top edge of the counter above the middle deck gun ports. My three principal sources, the Payne print, Willem van de Velde sketch, and the Lely Portrait of Peter Pett all seem to show the top of the counter terminating at level of the top of the middle gun ports. Looks like more demolition of the stern is in order.
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