Dear Querist,
For tenancy rights/pagdi rights, if no proof of original pagdi payment is available, the cost of acquisition may practically be taken as Nil. The option of taking FMV as on 01.04.2001 is generally not available for tenancy rights if the cost cannot be proved.
Section 54F may be claimed if the conditions are satisfied. Section 54EC is generally available only for transfer of land/building or both, so it may not apply to pure tenancy rights.
Your father-in-law may pay tax on the taxable LTCG and gift the balance amount to your wife. Gift from father to daughter is not taxable in her hands; keep a proper gift deed and bank trail.
For a more detailed review of your case, you may book a phone consultation.
CA Shubham Goyal