Tolerance allocation standards do not exist formechanical systems with flexibility and whose response aretime varying, subjected to discontinuous forcing functions.Previous approaches based on optimization and numericalintegration of the dynamic equations of motion encounterdifficulty with determining sensitivities around the forcediscontinuity. The Alternating Frequency/Time approach isapplied here to capture the effect of the discontinuity. Theeffective link length model is used to model the system and toaccount for the uncertainties in the link length, radial clearanceand pin location. Since the effective link length model isapplied, the equations of motion for the nominal system can beapplied for the entire analysis. Optimization procedure isapplied to the problem where the objective is to minimize themanufacturing costs and satisfy the constraints imposed onmechanical errors and design variables. Examples of toleranceallocation are presented for a single cylinder internal combustion engine with a flexible connecting rod.