I think it's really nice looking the way it is! Go with a new seat first and see if that doesn't do you for a while. I do not know if there is enough room to re-sculpt the seat as you are proposing. That is right over the battery box and the only thing I can see that will give much is the padding.
I have a Corbin that I picked up on eBay a few years back. It needed modification before it would even fit! I had to grind the front tab, expand the holes in the rear, and sand off high spots on the seat pan. After all that work it is still kind of a trick to get off. It does look nice but you know what? The original is actually more comfortable imho. I kept it and may have it recovered one of these days.
Back to your 906, I think the way it looks now is grand. That being said, it is your bike and if new paint is the only thing that works for you then do it. (I confess that I would like to build a spare set of pannels for my 750 and then have 2 Pasos for the upkeep price of one.

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BTW - It is great fun to play with graphics on the computer and a whole lot cheaper than actually painting the bike. Keep doing that till you get a look that really turns your crank.