David,
At the risk of bringing the discussion back to the subject matter of your post and question, and on the assumption that you are researching and writing “Wellington against Napoleon”, I can only say that I hope that Patrice Gueniffey, Bonaparte 1769–1802 (translated by Steven Rendall) is in your bibliography.
http://www.hup.harvard.edu/catalog.php?isbn=9780674368354&content=reviews
You will note that despite the time-span of this first volume of this biography, and the title chosen, Gueniffy refers both to Napoleon and Bonaparte on the first and last pages and throughout the work.
So I would personally prefer you to opt for Napoleon, using Bonaparte when necessary for example referring to specific instances during the periods when he was military student, general, consul etc. It may perhaps be useful to consider, that the personality / character of Napoleon the Emperor pre-existed his elevation to (some would say, seizure of) absolute power and so not necessarily time-bound to the period following his coronation.
Setting aside the natural demarcation of 1804, and the obvious weight of events post coronation, I hope you will have an even focus on specific “moments” such as 1793, 1799, 1801-2, 1805, 1807, 1809 etc.
Shame volume two is not yet out as will provide a very useful additional source.
Best wishes
A