Determining the number of propagating degrees of freedom in metric-affine theories of gravity requires the use of Hamiltonian constraint analysis, except in some subclasses of theories. We develop the technicalities necessary for such analyses and apply them to the Weyl-invariant and projective-invariant case of metric-affine-R theory that is known to propagate just the graviton. This serves as a check of the formalism and a case study where we introduce appropriate ADM variables for the distortion 3-tensor tensor and its time derivatives, that will be useful when analyzing more general metric-affine theories where the physical spectrum is not known.