Regarding applicability long term capital gain

1. In your case, the sale of Residential property will attract capital gains tax depending upon the period of holding. 
2. Considering LTCG, Mr. A needs to pay tax @ 20% after deducting indexed COA from Rs. 16,00,000. Where residential property was sold, the exemption available are,
i) To invest in new residential property before one year from the date of sale or within 2 years from the date of sale or construct within 3 years from the date of sale ( Sec 54) 
ii) Invest in bonds such as NHAI, REC, PFC, IRFC within 6 months from the date of sale ( Sec 54EC) 
3. In your case, there will not be any exemption available and tax need to be paid on LTCG @ 20%. 
4. If its an STCG then it will be taxed according to slab rates available. 
5. And in your case time limit for filing ROI expired, you may pay a penalty of sec 271F of Rs. 5,000 and the income will be assessed to tax u/s 144 (best judgment) and prosecution proceedings may be initiated u/s 276CC. 
Please correct me if the above solution has an alternative view. 

1. Fair Market Value (FMV) as on 01.04.2001 is to be ascertained. IT is to come up with the best possible solution for arriving at FMV as on 01.04.2001. However, the suggestion would be to get the valuation from a Chartered Valuer of the property as on 01.04.2001. 
2. After arriving at FMV compute indexed COA using the indexation table and then arrive at LTCG. 
Please correct me if the above solution has an alternative view.