Anders states that the Final Five left Earth in a ship traveling at near-light speed, mentioning the relativistic effect of time slowing down for those aboard. It's stated in earlier episodes that the holocaust on Earth took place two thousand years ago. Given that amount of time, the Final Five's ship could have only traveled less than two thousand light years from Earth before they encountered the cylons. This is inconsistent with other distances mentioned in the series.
Brain surgery is typically performed while the patient is awake so that loss of function can be perceived and hopefully repaired during the surgery. Sam was under general anesthesia during his surgery, and as a result the surgeon did not notice a problem.
No-one knows how final five did look, there is no HUB and still Ellen is resurrected. Where did a body come form if nobody knew that Ellen is a Cylon.