One correction, Rhaegar's mother was Rhaella, not Rhaenys.
Arse
You think Rhaegar secretly married Lyanna? If he did so openly there has been no mention of it. And if he did marry her, why did he not produce her, the septon, the witnesses and the bedsheets? Proving that he married her may and having Lyanna plead with Eddard may have gone a long way to stopping the rebellion. This is one of the real sticking points for me.
It's worth noting that we have no evidence of polygamy in the Targaryen family after Aegon IV. It may be that it was outlawed after Aegon IV's time and Rhaegar wanted it kept quiet. Agreed though that if he did marry Lyanna, announcing it openly may have helped avert the situation.
OTOH, Brandon and Rickard may have been burned and the rebellion underway by the time he married Lyanna.
Do you think that Elia was seen as not just being frail after Aegon's birth, but terminally ill?
It's a possibility. We are told, repeatedly, by Oberyn and others that Elia was quite frail and weak, and we know that childbirth is a risk and a big deal in this society even for a fully-healthy woman.
You said that Rhaegar hightailed it to Winterfell and took Lyanna. I thought Lyanna was at court in KL at this time. You're saying he pulled a Bael the Bard on Rickard?
I've never heard that Lyanna was in KL. Why would she be? I've seen theories that she may have been with Brandon at Riverrun and that's where Rhaegar grabbed her, but the general opinion seems to be she was Winterfell. Of course, ravens would get from Winterfell to the Eyrie (where Robert and Ned were) or to Riverrun (where Brandon was) before Rhaegar could even get to the Neck, possibly allowing others to intercept him, so you raise an interesting point here.
Are you saying that Dany's eggs were the very three that the Targaryen's tried to light at Rhaegar's birth or are you saying they were from the same clutch? I've not read any Dunk'n Egg.
No, they are the same eggs. The eggs themselves aren't mentioned in Dunk 'n' Egg (or at least the two stories published so far) but they are mentioned in GRRM's descriptions to Amoka of the Princesses in the Tower (the sisters of Baelor the Blessed, whom he locked in the Maidenvault in the Red Keep so they wouldn't tempt him with carnal thoughts).
The last Targaryen dragon was a stunted green whose clutch of eggs did not hatch. The eggs remained heirlooms of House Targaryen, but no-one could hatch them. Baelor the Blessed prayed over them for a week and nothing happened. He left them in the Red Keep, but it looks like that his younger sister Elaena got her hands on one of them:
Her hair was a platinum white with a bright golden streak down the middle, an unusual color even for the Targaryens. Elaena's most cherished possession was a dragon's egg whose stony shell showed the same colors as her hair. -
GRRM's description of Elaena Targaryen
Compared with:
One egg was a deep green, with burnished bronze fflecks that came and went depending on how Dany turned it. Another was pale cream streaked with gold. - A Game of Thrones
So we can gather that the three eggs were laid by the last Targaryen dragon who was allegedly poisoned by King Aegon III, the Dragonbane (aided, according to AFFC, by the maesters of the Citadel). Nine mages came from the eastern lands to hatch the last eggs, but failed (presumably why Aegon III didn't just destroy the eggs: he thought them useless but with possible worth as trinkets). The eggs passed down through the Targaryens, none of whom could hatch them. It looks likely that after Baelor gave up on them, his sisters kept them as ornaments.
The three eggs next turn up in the Blackfyre Rebellion, when we learn (in
The Sworn Sword) that a friend and agent of Daemon the Pretender, Quickfinger, tried to steal them from the Red Keep but was apprehended.
It has ben speculated that the three dragon eggs were taken across the sea with Daenerys and Viserys when they were infants and perhaps kept by Ilyrio Mopatis for his own ends. In a way it was actually a crap wedding present, because the eggs were rightfully Dany's anyway