Flame wont stay on and have replaced the flame sensor

You have a limit switch that is tripping. I bet it is the flame roll out switch that is very close to the burners. You can bypass this switch to check if it is the one causing the problem by removing the two wires going to it and installing a small jumper wire between them. If the unit starts up, then that's the problem and if not, check all of them. But that's pretty much the only thing it can be. But, you need to double check that the unit is being told to come on and not cutting out intermittently. I doubt it though!