Thanks for pointing out those descrepancies in the instructions. I personally haven't been worrying about the painting instructions on this kit. My knowledge of the subject matter allows me to paint by memory.
The kit directions only tell part of the story. These aircraft get parts changed out so often that leaves a few options when it come to many parts. One example is the main and tail rotor heads. The kit instructions say to paint the main rotor head assembly grayish blue for the 1st marking option. In reality, most rotor head assemblies are either black or the lighter tacticle gray. Some rotor head assemblies have 6 black sleeve and spindles, but one grey one. Like the one in this picture taken during the invasion of Iraq.
You'll see the sleeve and spindle assembly next to the crew chief's right hand is gray, but the rest are black.
The kit instuctions say to paint the tail rotor head assembly gray, which they often are gray. However, just as many have all black tail rotor heads. Here's a pic of a gray one. Sorry I don't have a pic handy of a black one.
CH-53E's have slight variations from aircraft to aircraft when it comes to how they are painted. Feel free to check out the reference pics on my photobucket site. I hope they help you out.
http://smg.photobucket.com/albums/v491/ridleusmc/
Semper Fi,
Chris