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
![](http://img573.imageshack.us/img573/4687/stitchoutput.png)
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:
![](http://img267.imageshack.us/img267/5209/originalshoreline.png)
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
![](https://img43.imageshack.us/img43/1971/finalwh.png)
Here you have ocean pattern. It can be stacked in both horizontal and vertical axis without any seams
![](http://img829.imageshack.us/img829/3730/waterpattern.png)