It looks like the easiest way to tackle it is to get all the bits separately, then assemble the complete front end (forks, yokes, front wheel etc). Then remove the old forks and slip the completed front end assembly into place. It means perhaps buying a second lower yoke with stem, but as Mike pointed out, then you've got the original bits still if you come to sell.
Part of the trouble with Mike's description of the actual task, is I don't think it really helps to decide which model of R1 to go for, but to be honest, I haven't read it that thoroughly yet. I mean, how much better would 43mm forks be over 41mm? Would such a difference be noticeable? And altering ride height and geometry can have drastic effects on handling so the different end results with different year set ups could also lead to quite different results in handling. Mike only really talks about the one set up (that he's using), how much different would the others be?
As I understand it, if you lower the front end on the forks, you're effectively reducing the rake (think that's right; steepening the steering head angle anyway) - yes, it makes the steering quicker, but usually has a downside of reducing high speed stability. Some people spend forever chasing one handling problem after another around their bikes because of one change like this. (You change front end geometry, something at the back is thrown out and has to be compensated for etc).
So still plenty for me to learn here before I commit to anything.