Question

How can i calculate drift velocity of charges in a conductor if it is not uniform?

Answer 1

You are right there. Drift velocity can be expressed in this form. But for conditions including a non uniform conductor liks this one, we prefer to use the other formula which is $v_{d} = \frac{-eET}{m}$ where E is the electric field and T is the relaxation time.
If you are looking for a way to use the formula $v_{d} = \frac{I}{neA}$ , you will have to integrate the cross section area of the conductor with the initial and final areas as limits. BTW these type of questions have a little chances to appear in any kind of examination.