Is it permissible for someone to make a supplication to Allah to marry an already married, or an engaged woman?
No, it isn`t, and the person who does so is sinful before Allah, The Almighty.
Should a person feel pleased, or have a virtuous vision after offering Istikhara (guidance prayer) in order to do what he/she had offered it for?
The result of the Istikhaarah is not necessarily that a person sees something (in his dream), or feels pleased, but the most important result of the Istikhaarah is whether a person is enabled to do a given matter or not.
Is it true that whatever is dry is pure even if there was impurity on it?
The impure material object does not soil (make impure) anything else unless the impurity is wet and transferable. But, if the impurity is dry or non-transferable, then there is no problem. Fuqaha has stated that: There is no disagreement between Muslim scholars that when a dry impurity touches something dry it does not make the latter impure.
How should I be kind to my atheist father?
Allah, The Exalted, has decreed and ordained his slaves to be kind with parents, even if they are polytheists, by honoring and obeying them in all that isn`t sinful, so that they might love Islam and embrace it as a result.