A fuel cell system having compression retention features that functions dually to provide compression retention and to provide structural sealing and vehicle mounting capability, eliminating the bulk of an additional structural enclosure while retaining the balance of plant simplicity associated with the use of structural enclosures. The fuel cell system has fuel cells disposed between a dry end unit plate and a wet end unit plate and a compression retention system with a pair of opposing end caps and a pair of opposing side panels such that wet end unit plate is fixedly secured to the opposing end caps and the dry end unit plate is adjustably secured to the opposing end caps. Methods for eliminating the effect of stack height variance and balance of plant tolerances on fuel cell system installation are also provided.