Ok Don,
Let me see how I can help.
1) First, reply to this question: "Do you have all the hull planking complete" ? First you must have all of your hull planking finished BEFORE you "cut-out" the Gun Port square openings. I see that some of the "Bulkheads" (part of the frame) goes through the openings of the Gun Ports. This is why you must have your model completely planked with the deck complete before you can cut out your Gun Ports. I do not know what stage you are - and I will wait until I can see a good picture of your ship so far.
2) Do you have the plans sitting in front of you? What size of sheet of paper did you print your plans or are you viewing the plans on your computer?
3) Is your Ship the same physical size as your plans? In other words, is your model the same length, width and height = the plans?
(if it is, then you can use a piece of cardboard as a template to copy the Gun Ports from the plans to your model !!!) If the plans are much, much smaller in size - then this will pose a different problem. You really need for the plans to be the same size as the model.
Most all kit plans are a 1:1 ratio. If you copy the plans to a 8x11 sheet of paper, then we have to do some converting.
4) I assume after all of this that what you are wanting to know is the DISTANCE between EACH gunport and also where to position them. If this is what you want to know, then we have to make a TEMPLATE from the plans and TRANSFER that template with the Gun Port Cut-outs and tape the TEMPLATE to your Model and trace out the openings with a pencil. Remove the TEMPLATE and use an exacto knife to cut out the square openings.
When you make the Template - make SURE you have a good reference point like the TOP EDGE of the RAIL of the ship.
Here is a set of graphics that I created that might be of some help.