The quantitative modeling and design of modern short-pulse fiber lasers cannot be performed with averaged models because of large variations in the pulse parameters within each round trip. Instead, lumped models obtained by concatenating models for the various components of the laser are required. Since the optical pulses in lumped models are periodic, their linear stability is investigated using the monodromy operator, which is the linearization of the roundtrip operator about the pulse. A gradient-based optimization method is developed to discover periodic pulses. The computation of the gradient of the objective function involves numerical computation of the action of both the roundtrip operator and the adjoint of the monodromy operator. A novel Fourier splitstep method is introduced to compute solutions of the linearization of the nonlinear, nonlo cal, stiff equation that models optical propagation in the fiber amplifier. This method is derived by linearizing the two solution operators in a split-step method for the nonlinear equation. The spectrum of the monodromy operator consists of the essential spectrum, for which there is an analytical formula, and the eigenvalues. There is a multiplicity two eigenvalue at \lambda = 1, which is due to phase and translation invariance. The remaining eigenvalues are determined from a matrix discretization of the monodromy operator. Simulation results verify the accuracy of the numerical methods; show examples of periodically stationary pulses, their spectra, and their eigenfunctions; and discuss their stability.