The nib on Japanese pens are thinner than those on European pens so a Namiki fine might be more like an extra fine european. This thin a nib can often times seem scratchy because, for lack of better technical knowledge, they are really thin. I have been told that when using an extra fine nib, you should try to put as little pressure as possible on the nib. This tends to reduce the scratchy feeling of the nib. The problem is that so many people (myself included) are used to using ball points that they find it hard to write with no pressure. I would suggest that you try writing with as little pressure as possible and see if it helps at all.
You could have also got a lemon. The nib might not be set up correctly which would explain the scratchiness. If there is a dealer close by, I would take it to the dealer and have them inspect it. If there is a problem, they will tell you how to send it back to Namiki, or they might do it themselves.
If you are filling the pen correctly, with the whole nib in the ink, I don't know why it would not fill up completely. You could try filling up with water and see if anything happens differently, or you could try putting more of the section into the ink to see if it makes a difference. You might also want to try moving the piston slower, I find that it takes in more ink if you move the piston slowly.
Good luck in getting your pen working, it is a beautiful pen and it should write beautifully too.
-Jesse