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.
Is permissible to buy/sell with non-Muslim?
Yes buying/selling for a Muslim with non-Muslim is permissible as regards what is lawful.
What should a sick person, who is incapable of fasting, and who didn`t make up for missed fasting days, do?
One who has missed fasting days is obliged to make up for them, but if he/she wasn`t able to because of an incurable disease , or old age, then he/she has to pay a ransom which is feeding a needy person for each of the missed fasting days. And Allah Knows Best.
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.