Praise be to Allaah.
Evil whispers during prayer and at other times come from the Shaytaan, who is keen to misguide the Muslim and deprive him of good and keep it far away from him. One of the Sahaabah complained to the Messenger of Allaah (peace and blessings of Allaah be upon him) about waswaas during prayer, and he said: “The Shaytaan comes between me and my prayers and my recitation, confusing me therein.” The Messenger of Allaah (peace and blessings of Allaah be upon him) said: “That is a devil called Khanzab. If he affects you seek refuge in Allah from him and spit drily to your left three times.” He [the Sahaabi] said, I did that and Allaah took him away from me.
(Narrated by Muslim, 2203)
Proper focus (khushoo’) is the essence of prayer. Prayer without proper focus is like a body without a soul. The following are two of the things that help one to develop the proper focus:
1 – Striving to think about what you are saying and doing, pondering the meanings of the Qur’aan, dhikr and du’aa’s that you are reciting; bearing in mind that you are conversing with Allaah as if you can see Him. For when the worshipper stands to pray, he is speaking to his Lord, and ihsaan means worshipping Allaah as if you are seeing Him, and knowing that even though you cannot see Him, He sees you. Every time a person experiences the sweetness of prayer, he will be more inclined to do it. [?]. This depends of the strength of one's faith – and there are many means of strengthening one’s faith. Hence the Prophet (peace and blessings of Allaah be upon him) said, “Of the things of your world, women and perfume have been made dear to me, and my joy is in prayer.” According to another hadeeth he said, “Let us relax, O Bilal, with prayer,” and he did not say, Give us a break from it.
2 – Striving to ward off the things that may distract you during prayer, namely thinking about things that are irrelevant or distracting. Waswaas affects each person differently, because waswaas has to do with a person’s level of doubts and desires and the degree to which a person is attached to other things or is fearing other things.
(From Majmoo’ Fataawa Shaykh al-Islam Ibn Taymiyah, 22/605)
With regard to what you say about the waswaas reaching such a great level that you have begun to experience waswaas that makes you think about Allaah in ways that are not appropriate, these are evil whispers from the Shaytaan. Allaah says (interpretation of the meaning):
“And if an evil whisper from Shaytaan (Satan) tries to turn you away (O Muhammad) (from doing good), then seek refuge in Allaah. Verily, He is the All‑Hearer, the All‑Knower”
[Fussilat 41:36]
Some of the Sahaabah complained about the waswaas that was bothering [?] them. Some of the companions of the Messenger of Allaah (peace and blessings of Allaah be upon him) came to the Prophet (peace and blessings of Allaah be upon him) and said to him, ‘We find in ourselves thoughts that are too terrible to speak of.’ He said, ‘Are you really having such thoughts?’ They said, ‘Yes.’ He said, ‘That is a clear sign of faith.’” (Narrated by Muslim). (Narrated by Muslim, 132 from the hadeeth of Abu Hurayrah).
Al-Nawawi said in his commentary on this hadeeth: “The Prophet’s words, ‘That is a clear sign of faith’ means, the fact that think of this waswaas as something terrible is a clear sign of faith, for if you dare not utter it and you are so afraid of it and of speaking of it, let alone believing it, this is the sign of one who has achieved perfect faith and who is free of doubt.”
And it was said that what it means is that the Shaytaan only whispers to those whom he despairs of tempting, because he is unable to tempt them. As for the kaafir, he can approach him in any manner he wants and is not restricted to waswaas, rather he can play with him however he wants. Based on this, what the hadeeth means is that the cause of waswaas is pure faith, or that waswaas is a sign of pure faith. See also question no. 12315
The fact that you hate that and your heart recoils from it is a clear sign of faith. Waswaas happens to everyone who turns to Allaah by reciting dhikr etc. It is inevitable, but you have to be steadfast and patient, and persevere with your dhikr and prayer, and not give up, because in this way you will ward off the plot of the Shaytaan. “Ever feeble indeed is the plot of Shaytaan” [al-Nisa’ 4:76 – interpretation of the meaning]. Every time a person wants to turn to Allaah, waswaas brings other matters to mind. The Shaytaan is like a bandit: every time a person wants to move towards Allaah, he wants to block the way. Hence when it was said to one of the salaf that the Jews and Christians say, “We do not experience waswaas,” he said, “They are speaking the truth, for what would the Shaytaan do with a house in ruins?”
(From Fataawa Shaykh al-Islam Ibn Taymiyah, 22/608).
The remedy:
1 – If you feel that you are being affected by this waswaas, say, “Aamantu Billaahi wa Rasoolihi (I believe in Allaah and His Messenger).” It was narrated from ‘Aa’ishah that the Messenger of Allaah (peace and blessings of Allaah be upon him) said: “The Shaytaan comes to one of you and says, ‘Who created you?’ And he says ‘Allaah.’ Then the Shaytaan says, ‘Who created Allaah?’ If that happens to any one of you, let him say, Aamantu Billaahi wa Rusulihi (I believe in Allaah and His Messenger). Then that will go away from him.”
(Narrated by Ahmad, 25671; classed as hasan by al-Albaani in al-Saheehah, 116).
2 – Try to stop thinking about that as much as possible, and keep busy with things that will distract you from it.
Finally we advise you to keep on turning to Allaah in all situations, and to ask Him for help, and to beseech Him, and to ask Him to make you steadfast until death, and to cause you to die doing righteous deeds… And Allaah knows best.
Islam Q&A
http://www.islamqa.com/en/ref/25778