I would highly recommend The Enlightened Soldier by Charles White. It is on Scharnhorst in the Prussian army before Jena. Clausewitz and the States by Peter Paret is excellent as is his Yorck and the Era of Prussian Reform, as well as Shanahan's book on the same subject. Owen Connelly's Napoleon's Satellite Kingdoms is excellent on Westphalia and Jerome, though he does give Jerome too much credit. Brendan Simms' The Struggle for Mastery in Germany is also very helpful.
There are four excellent books by Jack Gill on the Campaign of 1809. The first is With Eagles to Glory on the Confederation of the Rhine contribution to the French war effort against Austria and the Austrian invasion of Bavaria. The other three books entitled 1809 is a three-volume study of the entire campaign from the Austrian invasion to the battle of Znaim. I have read nothing better on the campaign.