Here are some problems many students encounter:
All of these problems are the result of pushing the head down or around rather than letting it move easily on a loose neck.
To improve these techniques, let gravity be your ally. For a deep meri, let your head fall forward -- don't push it into position. When executing furi and yuri, let your head roll around smoothly. It drops and then swings back up like a pendulum.
If your neck is stiff, it may be helpful to practice head rolls without your shakuhachi, or while holding it to your mouth without blowing.