1. Let new flat be registered in your name because having it named in your mother's favour and then transferring it to you, will involve another procedure of transfer. So make it direct. More so when your mother, you and others have mutually decided on distribution
2. You will have to pay capital gains tax in India as property will be in India. If you sell it within 3 years, you will be liable for short term capital gains tax and above 3 years, long term capital gains tax. As the flat will be in your name, whether or not your mother is living at time of sale, is inconsequential
3. You can very well make a bequest in your Will for the flat in favour of your son. You can also gift the flat to him in your lifetime itself. Latter option is better as the Will would be open to challenge when it is put up for poof for its genuineness. Your son being a US citizen doesn't matter
4. STCG and LTCG taxes are based on market value of property or agreement value, whichever is higher. Black component can be any excess sum being paid above circle rate. LTCG tax is @20% and STCG is at 30%