The body learns through repetition. When you attempt to apply a new technique, it is likely you will fumble as you consciously walk through the steps. Once the body has repeated it enough times, the movement becomes natural and fluid.
The idea behind performing kata is to train the body to move in specific ways. If the kata is appropriate to the system, the actual combative techniques are based on the habitual movements you develop.
This is why certain systems clash and should not be trained simultaneously. For example, if an attacker throws a punch at your head, you must either block with a karate technique or a boxing technique. The two are significantly different. Trying to decide which to use at the last moment will result in no block at all.
When you are already familiar with a particular style of fighting, it can be very difficult to make a transition to another. This is most true when the two styles are drastically different. Much like learning a second language, there is a tendency to retain an accent of the original style even after years of studying the new one. If you decide to always use a western boxing style cover or parry, then stick to shadow boxing and forget the kata. It will only serve to confuse your body.