This is a problem of teaching, IMO.
I've found that learning the kata and looking into it on your own is an inefficient way of understanding the nature of the applications for the kata. You can do that, but you'll end up wasting a lot of time chasing dead ends. That said, here is how I've come to understand how the kata used to be taught in order to pass on the applications and understanding of it's nature.
Students would begin practice with conditioning so that they would be physically fit enough to defend themselves. Some styles of karate specifically trained in weight training and you can find the old photos of the old masters in their students lifting clay jars with their finger tips, using barbells with concrete weights, and doing regular calisthenics. Some kata are actually designed to be performed with weight training implements! All of this physical training depended on the teacher. Some teachers valued it more than others. Then, they would move to learning basics and conditioning the body to perform the basics. Makiwara training was part of this, but also so was learning how to fall, and stay balanced. Then, students would start learning simple attack and defense routines in the form of drills. They would practice these drills while the teacher watched and the teacher would help each student perform them in such a way so that each student could use his own physical attributes. After a while, the teacher would start to introduce some new concepts and new responses that could be added onto the simple drills they learned so that they could start to see options and follow up techniques. Then, the teacher would provide the students with opportunities to improvise on these concepts against partners who would resist to varying degrees, letting the students see what worked and what didn't, allowing them to go back to training in techniques/concepts that needed improvement. Finally, the student would be taught the kata. When the teacher felt that the student had a good understanding of all the movements and techniques, they were given a single person exercise that helped them remember everything they were told.
Think about this method as you train. I think it's important to understand how your training diverges from this order, especially as you become older and more experienced. As you start to become more independent with your training, you can start to form your own training regime that will start to fit this. Or, perhaps you can go out and find a teacher who teaches like this. It's up to you.