Cycle Works makes the tools you need to get the outer bearing races out of the frame.
http://www.cycleworks.net/index.php?main_page=index&cPath=29_33_50I'm not sure, but I think I would leave them in the frame until after it is painted, that way their seats don't get painted.
I have the tools for pulling both the swingarm and steering head outer races. The swingarm works great and easily.
The one for the steering head is a little tougher, but it works great on the top one, and if your frame is stripped so you can turn it upside-down, it makes the lower bearing race a lot easier.
To remove the old lower bearing & inner race, I just used my rotary cutting tool and carefully cut it apart. You will need a new dust shield for that lower bearing, no matter what.
To install the new one, I put my triple-tree in the freezer for a while (no fork legs...). That shrunk the steering stem enough to slide it right on. Don't forget the dust shield, first!
Yes, the bearings are commonly available at bearing houses.