My main source of confusion is the following.
Suppose I have a scalar potential $V(x,y,z)$. The electrostatic field for this potential is $ -\vec{E} =\vec{\nabla}V = \frac{\partial{V}}{\partial{x}}\hat{x} + \frac{\partial{V}}{\partial{y}}\hat{y} + \frac{\partial{V}}{\partial{z}}\hat{z}$. This is a covariant vector.
The electric field can also be expressed as $\frac{m}{q}\vec{a}$ where $\vec{a}$ is the acceleration of a charged particle of charge $q$ and mass $m$ placed in the electric field. Since acceleration is a contravariant vector in writing $-\vec{\nabla}V = \frac{m}{q}\vec{a}$, aren't we equating a covariant vector on the L.H.S to a contravariant vector on the R.H.S when expressed in the same basis. So if we apply a transformation of the basis on both sides of the equation the two sides should behave differently. What am I missing?