When I am working on learning a new shakuhachi passage one of things I find that helps a lot is to break down more complex fingering combinations. I start by analyzing the piece and finding the best places to seperate the line. After I have it broken down I practice the one fingering transition until it is smooth then I practice from where I left off and start practicing the next part of the line. After I have the parts down and the fingering correct I link up the parts of the line to make the line whole. I also play the line in time but slowed down to make sure the technique is accurate as well as the pitches are accurate. From there speed it up as I can continue to keep it all together. At the point where anything starts to break down I slow it back down and make sure I am playing it perfectly. If you practice the sections perfectly instead of just playing it through however it comes out the piece will not only sound correct but the level of your playing will come up signifigantly.

Example:

Here is a line from Honshirabe:

To start you would play the U and make sure it is in pitch and then drop down to U dai meri. Practice making that transition until it is smooth and in pitch. Then practice going from U dai meri to Ri. Make sure you are raising your head high enough to get Ri in pitch when you make the transition. Then you can tie the U to U dai Meri to Ri all together and make it smooth and in pitch. Then practice going from Ri to Ro kan and so on until you have the line smooth and in pitch at the correct speed.