The first step for any charitable institution is to get itself registered under sec 12A with the Commissioner. Definitely 80G would be granted only if the trust is 12A registered. 12A also has a limitation period before which it should apply for registration - presently one year from date of creation of trust. Delays can be condoned by the Commissioner on proving good reasons. But after the amendment some years back, commissioner does not have power to grant retrospective 12A registration - even if he condones the delay.
Therefore the periods prior to the financial year in which the 12A application is made would be exposed for the trust in that it would be assessed as an AOP - if no definite shares are prescribed then at maximum Marginal rate ( of course if it has net taxable income above threshold limit). FCRA registration is an independent process with the Ministry of Home, Govt of India, and has technically nothing to do with 12A or 80G. But now a days FCRA is granted only if the trust has atleast 12A registration. 80G is not being insisted upon.