I think colours are really better this way !

For the changes you have to make, I would suggest you to use layers with Photoshop : much easier when you only have to change or re-make ONE thing on the map, instead of re-make it on the whole... I think about your mountains that your shrunk ; maybe it would be more beautiful if you remake them completely instead of pasting some shrunk mountains onto big ones...

I don't know if I'm clear