One of the difficulties that students sometimes encounter is that their in-breaths are noisy or hurried, or that they have a desperate quality to them.
Of course there are places even in honkyoku that require a quick breath so as not to break the phrasing, but in many cases there is no hurry. At first, just be with the in-breath when it's in-breath time: don't worry about what comes next, don't try to remember what comes next no matter how difficult it might be, just rest in the current moment with the current in-breath. That way you can do it as quietly as you want. Once you're used to this feeling of calm quiet on the in-breath, it is easy to change its length without any "gasping" quality.
I also believe that the human will to live can impose a desperate quality to the in-breath, as if we have to work feverishly at getting enough air. We also tend to think of the in-breath as work and the out-breath as release, but this habit can be reversed. There is an exercise I like to do that demonstrates the autonomic security of the in-breath: expel all the breath from your lungs. Then expel some more -- you probably really haven't gone anywhere near the end of your breath. Hold it down there for a while. Then just let go. Notice how air automatically rushes into your lungs just by relaxing, without any work. I think it helps to remember this feeling while playing.