In Principia Newton presents a picture based on forces rather than energy and momentum, and he did not have the concepts of vector and of mechanical energy at his disposal. Moreover, Newton opposed Leibniz's idea of putting kinetic energy ("vis viva") at the center of dynamics on philosophical grounds, because he considered forces to be more fundamental. There was no notion of potential energy at the time, and some of the forces treated in Principia, such as air resistance, are not potential, so when they operate even total mechanical energy is not conserved.
Conservation of kinetic energy and momentum was mostly considered at the time in the context of elastic collisions, and there was "vis viva controversy" as to which of them was the "true" quantity of motion. Neither could be considered a universal law at the time, because the nature of heat was not understood, and frame dependent components of a vector were not an item. In fact, Newton worked with two different notions of momenta, mass times speed, going back to Descartes, and the modern one, but only in terms of components. He explicitly notes that Cartesian "motion may be got or lost", and derives conservation of components from the third law of motion:"if the bodies meet with contrary motions there will be an equal deduction from the motions of both".
In an anticipation of modern view Boscovich in 1745 characterized vis viva as the measure of force acting through a distance, and momentum as the measure of a force acting through a time, and D'Alembert included this characterization into the second edition of his Traite de Dynamique (1758). But neither the concept of a vector, nor the general notion of energy, required to give conservation laws centrality in physics, emerged until the 19th century.
As for use of calculus, there is evidence that Newton originally worked out Principia in terms of Euclidean geometry, and connected it to calculus only after the first publication. Conversion of Principia into the calculus notation was done by Euler in Mechanica (1736). Lagrange in Mecanique Analytique (1788) introduced potential energy (without the name, proposed by Rankine in 1853), and explicitly derived conservation of mechanical energy from Euler's reformulation in essentially the modern way. Modernizing the notation, Newton's second law $m_i\frac{d^2x_i}{dt^2}=-\frac{\partial U}{\partial x_i}$, where $U$ is the potential of forces, is multiplied on both sides by $\frac{dx_i}{dt}$ and summed over the (generalized) coordinates. Using the product rule on the left, the mutivariable chain rule on the right, and moving everything to the left gives:
$$\frac{d}{dt}\left(\sum_i\frac12m_i\left(\frac{dx_i}{dt}\right)^2+U\right)=0,$$
i.e. the sum of kinetic and potential energies is conserved.