How should I deal with the whispers of the devil with regard to ablution and purity?
Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it permissible to make up missed prayers at the times in which praying is disliked?
All perfect praise be to Allah,The Lord of The Worlds It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.
Is prayer mandatory on a dying person who goes through a state of unconsciousness, then wakes up?
If he wakes up and was conscious, then he should pray the way/manner he could, but if he wasn't, then he is exempted from obligatory prayer as Allah Says in this regard (What means): "On no soul doth God Place a burden greater than it can bear." [Al-Baqarah/286].