Nautical experts generally believe that there is a severe limit to the size of wooden sailing ships.
Here is a link to Wikipedia's list of the largest sailing ships of all time:
Some of them were steamships with masts and sails for propulsion in case the engines, failed, and others were or are sailing ships with engines to use when there is no wind. And some were pure sailing ships.
Judging by the sizes of the ships on the list, it might be possible to build sailing ships a thousand feet long or longer which sailed well under sail.
The bad news is that all the longest ships on the list were made out of iron or steel.
The list of the longest wooden ships ever built has much shorter ships. All of the longest wooden ships had structural problems, even though most of them had iron or steel structural parts to strengthen them.
So if you want to make a thousand foot long wooden flagship to dwarf the 150 or 200 foot long ships of the line, you have a problem.
The list of very large wooden ships which are claimed but poorly documented is interesting.
If some of the largest on that lists were real, the builders should have found some ways to overcome the limitations of wooden ships which seem insurmountable to modern people.
One thing that you could do would be to reduce rough weather in the waters where your supersized ship operates to ease strain on the wooden hull.
I note that the Great Lakes are large enough to have fierce storms and giant waves. So perhaps the fleets operate in a group of large lakes which ae all connected, and all large enough for even the largest ships to maneuver in, but which are not large enough for the winds to build up large waves before the waves reach the shore.
Perhaps the lakes are all long from north to south and the winds blow from west to east, for example.
Or maybe the naval battles are planned to be fought in a long but narrow strait without room for large waves to form.
Some some very large wooden ships were allegedly use in naval battles in Chinese lakes and rivers.
The length of ships is usually measured by the length on deck, the topmost deck going from bow to stern. Another measurement, the length overall, is the total length of the ship including poles extending from the hull.
And the length of a bowsprit sometimes approached 100 feet.
Some old sailing ships had a platform on the bowsprit with a mast and sail, thus adding another mast to the ship and extending the length of the sails. It was called a sprit topmast.
And this depiction of the English royal carrick Henry Grace a Dieu shows it with what could be called a "sternsprit", though it isn't as long as the bowsprit.
So naturally I can imagine a ship which has a platform, a mast, and a sail on such a "sternsprit" as well as on the bowsprit. I think that such a ship would be very impressive looking.
And possibly a super ship could extend its width with "sidesprits" with platforms, sails and masts.
There are claims that the allegedly gigantic largest Junks in Cheng He's fleets had two rows of masts in a zig-zag pattern, so you are not the first to think of having more than one row of masts.
The vessel which allegedly had the most masts was probably a raft built by Roman solders during the Republic to escape from Sardinia or Corsica. From what I remember it supposedly had dozens of masts and sails. So it probably had more than one row of masts. Since those Romans were not expert shipwrights, it broke apart at sea.
You say your shop should be propelled by sails or
muscle power, in the form of oars or hand cranked wheels.
Hand cranks are probably not the best methods, since men's legs are stronger than their arms. That is why there are little boats powered by bicycle like foot pedals instead of hand cranks. You might want to consider large wheels, like those used to pull up anchors, turned by men or draft animals, as the power source for paddle wheels or propellers.
Or you might want to use treadmills to power the paddlewheels, as on Chinese paddlewheel vessels.
I note that some types of sails are rigged so that they can swivel and change their orientation, to take advantage of changing wind directions. And it is possible that some of those sails had booms almost a hundred feet long. And if their masts were near the sides of a ship instead of the centerline, they could extend far beyond the sides of the ship, and thus make the ship much wider if booms are counted.
There is speculation that some allegedly giant ancient wooden ships were catamarans, with two hulls side by side.
During the 1850s a ship was built called the connector with separate hulls from front to back, connected by giant hinges.
So maybe your super wooden flagship could have three to five sections, for example, each 150 to 300 feet long, and thus a total length of 450 to 1,500 feet, not counting the hinged spaces between the hulls.
And possibly you might want to consider having several connected hulls side by side and front to back.
And these are some suggestions for trying to overcome some of the problems with building super large wooden ships.