What you describe is a known problem. FT has a number of issues with processing things across the -180/+180 longitude line, because that's where FT's editing data has a discontinuity. The only way that comes to mind to fix those holes is to paint over them with a small brush. Start with Tools>>Actions>>Normalize Data before painting to ensure that the holes aren't composed of something nasty like infinities or not-a-number values because those two classes of numbers can't be painted over. Then use the Tools>>Paint Values>>Land Offset tool to get a paintbrush to paint over the holes. Use the mouse wheel to quickly change the tool size to a small one. The hold down the Shift key and click on a nearby point to pick up a land value close to what you need to fix the current hole. Finally, click on the hole and it should be filled fairly closely to the desired value. Repeat until the holes are filled.
If you choose to start over (using Map>>Next World and Map>>Previous World to reset the map editing data without ), I recommend using the Longitude value on the Secondary page of the Map>>World Settings property sheet to rotate that line around until it mostly intersects ocean. The mapmakers here on Earth did that and it's worked out pretty well.
FT unfortunately doesn't provide facilities to directly import and export editing channels and it also doesn't provide facilities to directly rotate the world in the software. At the moment, You're pretty much limited to exporting the height field to a third party tool as an image, editing it there, and then importing it again into FT ( see http://www.fracterra.com/ThereandBackAgain/index.html for an example of how to do this with the previous version of FT, but it should all still apply ). This technique pretty much loses the dynamic fractal part of the operation, but it allows you to keep the general shape of a world that you've invested a lot of effort into.