#SPOILER# I have seen it! LV426theory #MAIN SPOILER#

How do you think they were turned into eggs?  Egg morph?

And during the ensuing years of solitude he becomes even more crazy, I suppose

Well, RS does not accept the queen, so that would be my guess. 

I think he hatches the embryos(the ones he placed in the draw at the end of the movie) and they 'sting' the colonist. And they morph into eggs.

Sorry, I think this is the same as another thread.

Sorry, I think this is the same as another thread.

Hmm...I like to think 'Awakening' will have to do with the nasty little surprise being revealed at the original intended destination of Covenant.

Even though RS doesn't like the queen, he shouldn't just ignore it. (It is part of the life cycle) 

"I believe that the ship is heading to LV426 and the "thousands" of eggs Kane saw in the Alien(1979) are the Colonist from the Covenant ship."

Except the egg silo was in a Juggernaut / Engineer ship in Alien. Obviously not the Covenant. So where does the LV426 Juggernaut come into this?

It would make sense for him to go back to where it started and to also acquire a new Derelict Ship. Thus, turning those colonist into eggs and then prepping a payload for earth. Yet, someone stops him, crashes the ship and sends out the warning signal. How that will happen and play out, who knows but I agree LV-426 and the system is important to the story.

I love the idea of those embryos becomes the eggs on LV426. But I am still unclear about the final shot. (Spoiler ahead...) Why does the story show two alien embryos instead of one? Also at the beginning of the movie, Walter takes out one human embryo, for what purpose?

(No spoilers here)
Apart from that, I must say I like Alien Covenant a lot. I am still digesting the storyline but overall I think this movie is a great step-up of Prometheus. I would say the character of David steals the show and leading this character into the original Alien saga is just fantastic. I can't wait to read the novelization of Alien covenant and will definitely see the movie again. 

Yea I'm guessing (as someone else previously mentioned on another thread and here) that David is heading back to 223 to grab another ship with a full stock of the pathogen.

Beyond this he probably will indeed use the colonists to create a payload of eggs and my guess is, at some point one of the Prometheus style engineers intercepts him or is sent to stop him. This engineer likely kills David but not before David infects it.

My thought exactly.