What is the way to get rid of the numerous intrusive thoughts that come during prayer and at many other times, and which cause a feeling of unease?

Part of a complete repentance is to make up for the missed prayers. The remedy for obsessive thoughts is to seek refuge with Allah from Satan, and to strive against oneself to abandon these obsessions and turn away from them, along with keeping company with righteous people, and maintaining presence of heart in prayer by contemplating the invocations and verses.