EDIT: I was looking up how much fuel a nuclear sub carries for the purposes of this discussion, so if you're reading this, wave at your friendly neighborhood NSA analyst.
I thought it was some sort of perpetual motion engine, hence the need to replace 'parts'. Honestly I suspended disbelief and wasn't looking to deconstruct the movie. If you want to get nitpicky you forgot or missed the MOST GLARING inconsistency...if the train had, what appeared to be a state of the art dentistry car, why in the hell did Tilda Swinton have a pair of choppers straight from the G. Washington line?
One thing you never want to have to confess...'I know what people taste like'. But seriously, I thought that was a very OLDBOY-esque moment, followed by Ed Freaking Harris in a kimono just continuing to pull the rug out from under our 'hero'. That, above all else, really sold the movie for me and allowed me to not dig so deep into unraveling the piece. Was it shaky? Sure...most sci-fi is. But I just kinda believe in the 'anything can happen' unwritten rule of the genre. Zardoz, Rollerball*...hell name a sci fi movie you cannot dismiss by applying real world rules to.
*yes, I understand these are not mainstream choices...sue me.
Response to SPOILER:
Fat is flavor.