1. #ffffff translates to 255 in grayscale (how the import is managed). You can scale that to whatever you like in Wilbur, however. Using Filter>>Mathematical>>Span with a Low of 0 and a High of 6000 will scale your map to the 0 to 6000 range you mentioned.

2. If you want rivers to follow a specific path, draw that path in there using a darker value than the underlying landscape. If you're using a coastal mask, make another map with rivers in black and use that mask for the first few iteration scales to force the rivers into the exact path that you want.

3. Make a sea mask that has land as pure white and ocean as pure black. Load that mask as a selection when doing operations like precipiton erosion to enforce your coastline. You can invert the coast mask and set the world to something like -20 to allow the edges of the terrain to erode below sea level (reload your original mask before doing your erosion). If you want, you can lower everything to get closer to sea level after your initial scaling.