All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
If a person is very afflicted with whispers, then he should repel them, and not pay any attention to them, and act based on what is predominant (i.e. on the most).
Therefore, you must ignore all these whispers until Allah spares you from this disease with His Grace. So, if you doubt whether you prostrated two prostrations or one, then consider it as two prostrations, and if you doubt whether or not you have recited Al-Faatihah, then consider yourself that you have recited it, and so on. If you make use of your fingers and the like, in counting the number of Rak'ahs, then there would be nothing wrong with that.
For more benefit on whispers, please refer to Fatwa 374308.
Allah Knows best.