Sounds like an awful lot of work - I'm impressed! As to the rivers I think jbgibson suggested that you might emphasize the main ones instead of getting rid of the smaller tributaries. It sounds like a better option to me.
Most of my time on this iteration of the map has been spent on developing a detailed greyscale elevation map thingy of the continent - after which it was dead easy to use a mixture of emboss and blur functions to generate the mountains. Then I added some layers to make the map more colourful.
I've drawn all the rivers by hand, using the elevation map thingy as a guide to ensure water only flows downhill. I admit to getting a bit carried away with the tributaries; I'm planning to cull a lot of them at some point ...