The free piston engine (FPE) is a type of internal combustion engine (ICE) with no crankshaft, so that its piston motion is no longer constrained by mechanical linkages. The FPE has a high potential in terms of energy saving given its simple structure, high modularity and high efficiency. One of the technical barriers that prevents the wide spread of the FPE technology, is the lack of precise piston motion control. Previously, a robust repetitive controller is designed and implemented to form a virtual crankshaft that would provide a precise and stable engine operation. The experimental data of engine motoring tests with virtual crankshaft demonstrates the effectiveness of the controller. However, the presence of a transient period after a single combustion event prevents the engine from continuous firing. This paper presents a modified control scheme, which utilizes a reference and control signal shifting technique to modify the tracking error and the control signal to reduce the transient period.