Which of the three things is better as an ongoing charity for the deceased: digging a well, or installing a water cooler in a mosque, or paying the expenses for someone else's Hajj (Hajj al-Badal), knowing that my father performed Hajj seven times?

The best ongoing charities for the deceased are providing water and building mosques. Providing water is among the best charities, as stated in the hadith (definition) of Sa'd ibn 'Ubadah: "Which charity is best? He replied: Providing water." Building mosques is also among the virtuous deeds, as stated in the hadith: "Whoever builds a mosque for Allah, even if it be as small as a bird's nest or smaller, Allah will build for him a house in Paradise." As for charity in the form of money or performing Hajj, these are virtuous deeds, but they are not ongoing charities whose reward continues for the deceased.