Removing rocker cover

[Gray fox]

Just checked the valve clearances on my bike and couldn't get the cover off without removing the water pipes. They are held in by the cap screws as you described. The pipes can be difficult to remove due to corrosion, expect a certain amount of crud to fall into the camshaft housing when you remove the cover, had to clean mine out with rags and a vacuum tool. The pipes are quite difficult to re-install, best done with some grease and a twisting action.
Good Luck