Capital gain

Could you explain what you mean by purchased in 1998 ? Do you mean you received the money in advance? As I know Unless the stamp duty is  paid & registration is done , we can't say property is sold officially .   so I guess  in this case year 2003 will be considered .

Aggreement and the payment made on 1998 on registration and stamp duty process taken palce on 2003

1998 COST INFLATION INDEX WILL APPLY 

Ownership shall be reckoned from the date of posession. So Cost Inflation Index of 1998 shall apply.

Year 1998 shall be taken for the purpose of calculating indexation.

As per the provisions of the income tax act, cost of acquisition shall be the price as mentioned in the agreement. If price as per agreement is less than the stamp duty value  assesed or assessable by the stamp valuation authority then stamp duty shall be paid on such value assesed.

Cost of Indexation is applicable on the year on which u get the possession of the Flat then u will be treat as the owner of the flat.

CII will be applicable for that year in which you have taken the possession on such property.