So I've played around PS little bit and I think I've solved your problem. Unfortunately shorelines has to be corected manualy, everything else can be automatized.
This came out from stitching screenshots together
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after repairing shorelines I've selected all blue pixels (with magic wand tool, tolerance 150,
AA turned off) then contracted selection by 4 pixels (in order to preserve original shoreline waves and details) and hit delete. Result:
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Then I've created new ocean from single screenshot. Water tiles are repeating in chunks 32x28 pixels with some random variations in wave pattern. And finaly whole sector with new ocean
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Here you have ocean pattern. It can be stacked in both horizontal and vertical axis without any seams
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