Oh, but where's the fun in that? My thinking in working on it at the continental shelf range is that I can use Fill Basins to fix the pits and divots at sea level, because Fill Basins won't stop at sea level like it normally does. It stops at the waterline, which is now much lower. So it will fix the errors at sea level for me.

I've gone around the edges of the continental shelves and trimmed them to look a bit more realistic. I didn't connect any of them together, even though that's realistic, since then I'd have to put in some mountains to simulate the continental collision. I didn't have to worry too much about the tiny pits or offshore islands, since they most likely won't affect anything once I move the sea level back up to 0.

Here is the new map:
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