Yea drain the oil and radiator fuild clutch cable and kick start. The reason the manual say remove the water pump cover is when your putting it back together you have to line the water pump shaft to the gear .So when you line it up by eye you grab the impellar and wiggle it back and fourth to get it to line up in the gear .Makes it alot easier to do. Un less you line it perfect, but if its not in  right  dont force  the clutch cover back on our you will have more problems.