A catholic I know wishes to marry a muslim girl who has spent the past year trying to teach him about islam. He was told that he can only marry her if he is muslim, and he is willing to convert. He believes in one God, however has some doubts about the Prophet Muhammad being a prophet, although he is willing to accept that despite having these doubts. He believes that it is impossible for someone to be 100% sure about anything, but still believes more than he doubts. Would their nikkah be valid?
Brother their Nikah will not be valid, in my opinion.
a) It is absolutely essential for him to have absolute faith in the Oneness of Allah AND on Muhammad (PBUH) as His last prophet, any and all doubt invalidates you from Islam as these conditions are fundamental.
b) The title of the question you pose itself is absurd - "taking Shahada with doubts", really? How can you 100% agree to something and be in doubt at the same time?
Allah knows best, wassalam!