I can help a little with the rigging questions. When the ship was at sea, there would be one sail set below the bowsprit. I don't want to insult anybody's intelligence, but the bowsprit is the horizontal spar that sticks out from the bow of the ship. Underneath it is the spritsail yard. That yard had a square-rigged sail set on it. I think the sail is actually there in the photo; it's furled so tightly that it's hard to see.
There's a lesson to be learned there. A lot of modelers make the "bundles" of furled sails way too thick. The bundle, as you can see from the sails that are furled in the photo, is actually extremely small - often smaller in diameter than the yard to which it's furled. In that photo the fore course and the mizzen appear to be missing (probably for maintenance reasons). The main course and main topsail obviously are there, and the spritsail may be; on my monitor I can't tell for sure.
The modern crew has taken a little license in furling the main topsail. In the seventeenth century it was customary to furl a topsail while standing on the top (the round platform at the head of the lower mast). The sailors would gather up the sail into a more-or-less vertical bundle and lash it to the heel of the topmast.
It's also worth noting that the furled sail is fatter in the middle than at the ends. That's because of the arrangement of the rigging that hauls the sail up.
The spritsail yard is cocked up at an odd angle. My guess is that the crew was worried that a truck or bus might collide with it. Normally the yard would be horizontal. Or it might be twisted in its parral and, along with the furled spritsail, lashed alongside the bowsprit.
One more point about that photo. Notice the wide variety of sizes of rope in the rigging. The standing rigging (the lines that hold up the masts) is, generally speaking, quite a bit heavier than the running rigging (which controls the yards and sails).
My recollection is that the rigging instructions in this kit are actually pretty good (though somewhat simplified). If you study them carefully you'll be well on your way to a good rigging job.
When it comes to color schemes, the sky's the limit. In the photo it looks as though the Mayflower II is undergoing a refinishing job; almost all the colored paint is gone. My suggestion is to take a look at the various paintings of the Mayflower, and take your pick.
Hope that helps a little. Good luck.