To answer your questions as best I can:
1) The points themselves are the same. I'm not sure about the points plate, but I'm pretty sure that's the same as well.
2) Correct on it being #40. It's been a while since I've looked at one but I'm pretty sure you should see daylight though it. As long as you're removing the carbs it might be a good ised to give everything a good cleaning if you haven't already.
3) Here are some pics of a 400 motor in a 350 Frame. The footrests have been moved back, possibly mounted like on the 400 (I dunno). They seem to have made a pivot for the shifter. The rear brake is certainly different (another 400f part?) I was able to kick the motor over once I moved that footpeg out of the way.
http://i158.photobucket.com/albums/t110/hoodellyhoo/019.jpghttp://i158.photobucket.com/albums/t110/hoodellyhoo/018.jpg

4) As long as you're using the 350 frame, I don't see why the stock 350 exhaust wouldn't fit. You would probably have to just experiment with the jetting and see what you get.
5) No clue. Like you said, the 350 and 400 cables are different but I don't know if it's just a matter of length or if their construction is a little different too.
Hope this helps