Validity of Hakone free pass

1. Does it covers 2 calendar days or 48 hours? If I arrive on 1st day evening, and leave on 3rd day noon, do I need to purchase 2 days or 3 days pass?

2. Is there a preferred pass that includes travel to Hakone from Tokyo and leaving to Kyoto?

Thanks you!

1. Does it covers 2 calendar days or 48 hours?

It is based on calendar days, not 24-hour periods.

2. Is there a preferred pass that includes travel to Hakone from Tokyo and leaving to Kyoto?

You could buy the pass at Odawara Station. You could theoretically combine that with a Japan Rail Pass, but you would need to travel more than just Tokyo-Kyoto, especially after the pass' price increase this autumn.

1.
As the previous answer said, Hakone freepass is not based 24/48/72 hours.
If you arrive in the first day and leave in the 3rd day, 3days pass may be the better option.

https://www.hakonenavi.jp/international/en/discount_passes/free_pass

The difference between 2 day pass and 3 day pass is 400 JPN(less than 3 USD).
Anyway, you can buy passes at Odawara Station, on Tokaido Shinkansen.

2.
Along this plan, the cheapest is probably
- JR ticket from Tokyo to Kyoto (and you can stop over any station on the way, of course, at Odawara)
- Hakone freepass from Odawara

Have a nice trip!