Please check the instructions again as to where the frames and gunports should be, since they should not conflict with each other if the kit manufacturer made the kit design correctly. I think something may be off position on your model, or you are plotting the gun ports in the wrong locations. I have dealt with gun ports being too close to frames before, but that was because I MOVED the gunports and changed the design of the model myself, and had to cut away the frame bulkheads to make room for gun carriages and rigged gun tackles. A kit manufacturer makes mistakes on occasion, but usually not ones that offer great conflict with parts interference. Since your model is a cutaway of a hull, a conflict between gun ports and frames is serious because it will be PLAINLY VISIBLE. So, my solutions to the problem will not work for your model. Check your parts locations and take measures and compare them to the model plans.
My model showing hull bulkheads relative to gun ports. Look how close the gun carriages are in sereval locations. Note that on my model the locations of the bulkheads are NOT the same as they would be on the real ship. Originally I assumed that the kit manufacturer made them so, but learned later than they were not. Guns on the lower gun deck were supposed to be fake cannon barrels sticking into pieces of wood, not complete cannon carriages, so when I desired to install complete carriages, Aither the wheels on one side of a carriage had to be made thinner or a section of the bulkhead had to be cut away to allow more space, before the first layer of planking was laid down.
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Carriages sat right up against bulkheads on this model, which would not be the case on a real ship. Frames would not be this close to guns, or the gun crews would not be able to operate the guns. This model was clearly designed to be viewed from the outside only, and the interior is totally hidden. Your cutaway model must reflect the actual location of frames and gunports.
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Check your work against Jeff-E's on the Model Ship World forum.
His build log is very detailed. It can help you find where things may be going off track on your model.
Posted October 24, 2013
Hi All,
After they were maked out and I was happy with the positon of them the gunports were cut out. This was done as per the instructions by drilling a series of small holes inside the marked lines and then carefully cutting out that section and finally finishing it to size with a file.