This paper describes the modeling of a two-stroke dual chamber free piston engine (FPE) running homogeneous charge compression ignition (HCCI) combustion with an embedded linear alternator and a hydraulic pump. Variable compression ratio of FPE enables multi-fuel operation. Furthermore, the addition of an electric generator and hydraulic pump ensure the engine to have both high energy density and power density. These three concepts combined, will make for a highly efficient and flexible approach for engine operation. However, the characteristic of FPE also brings challenges in engine control. We propose a control oriented model that provides detailed gas exchange processes between intake/exhaust and cylinder volume, and the dynamic interactions between combustion, the linear alternator and the hydraulic pump. Influences of fuel and valve timing on engine performance are studied. Simulated engine dynamics are observed to have significant differences from conventional internal combustion engines.