Is there a consistent way if jumping over Bowser in the last Castle? I know practicing will help, but I want to know if there's something that makes it easier that I'm not doing.

do a slight turnback in midair and land to the right side of bowser junior. it significantly increases the frame window of the jump

Like wah said, you need to hit the right half of Bowser Junior. So start running right for a little bit, do a medium jump, press left to slow down and make it easier to hit the right side, then press right again after bouncing off BJ. If you have video of some of your attempts at it I can tell you what you're doing wrong.