Hi Sam,
Welcome to the wonderful world of Skorpion ownership. I hope you enjoy it as much as other Skorpion owners do.
Firstly, manuals. You can download most things you'll need from the 'Technical' page of my website
http://www.mzskorpion.net The paint shouldn't be too bad. I've had my Skorpion reprayed using 'normal' automotive paint, and the sprayer had no problem with it. As far as I'm aware, all paint colours used on Skorpions are the same as those used by Volkswagen, (at least on models sold in Europe), so your local VW dealer might be able to help.
As for the rear passenger seat, it could be worth asking around some of the people who have raced Skorpions, they might have one spare.
As for the carbs, unless you are going racing, what is actually wrong with them? OK, the design is a bit weird, but you've got them, they are fairly easy to set up, and they work! Adapting something from another bike is undoubtedly going to be difficult, frustrating, and after a lot of trying, possibly not any better that the stock set up. (Other contributers - feel free to disagree!)
Only thing I would say about the stock carbs is beware of the 'hidden' internal filter. If this blocks it can cause all sorts of misfiring and bad running problems - always fit an inline filter to the fuel pipe.
Hope you enjoy your Skorpion, and keep us up to date with any news.
Norman