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We develop a formalism to compute the statistics of the second largest eigenpair of weighted sparse graphs with $N\gg 1$ nodes, finite mean connectivity and bounded maximal degree, in cases where the top eigenpair statistics is known. The problem can be cast in terms of optimisation of a quadratic form on the sphere with a fictitious temperature, after a suitable deflation of the original matrix model. We use the cavity and replica methods to find the solution in terms of self-consistent equations for auxiliary probability density functions, which can be solved by an improved population dynamics algorithm enforcing eigenvector orthogonality on-the-fly. The analytical results are in perfect agreement with numerical diagonalisation of large (weighted) adjacency matrices, focussing on the cases of random regular and Erdős-Rényi graphs. We further analyse the case of sparse Markov transition matrices for unbiased random walks, whose second largest eigenpair describes the non-equilibrium mode with the largest relaxation time. We also show that the population dynamics algorithm with population size $N_P$ does not actually capture the thermodynamic limit $N\to\infty$ as commonly assumed: the accuracy of the population dynamics algorithm has a strongly non-monotonic behaviour as a function of $N_P$, thus implying that an optimal size $N_P^\star=N_P^\star(N)$ must be chosen to best reproduce the results from numerical diagonalisation of graphs of finite size $N$.