The part order goes as follows: nuke, coupler, coupler, service bay, service bay, battery, battery, coupler, coupler, sci junior, reaction wheel, hitchhiker can, and another set of couplers on either side attaching the engine/ tanks assembly. And I have made sure the engine is on. I've played around with about every setting and made sure that all the couplers displayed "disable crossfeed" (this disable and enable toggle thing is kinda confusing) on both sides of the pair.