So I'm going to attempt a mod on Jills that are laying eggs to spawn new (baby) dragons. What would I need to do to try to make this as lore friendly, or lore aware, as possible?

Well right off the bat- dragons don't lay eggs or give birth in any conventional sense. They're immortal spirits - a precise number of them came into being at the birth of the world and that number has remained constant (give or take some dragons slain and resurrected in between) ever since.

But then why are there Jills and if they are immortal spirits why do they leave physical remains and why were there dragonlings in Daggerfall? I'm not trying to be flippant or challenge you, just trying to get a better understanding of the subject as I tried looking for more information on them on Google but couldnt find any.

Dragonlings are just giant reptiles that look like dragons, but are unrelated, as stated in There Be Dragons.

Jills are ethereal feminine dragons that only appear during Dragon Breaks to mend time back into a linear state. The dragons of flesh-and-blood seen in Skyrim are not Jills, but are still a form of lesser Aedra, having broken themselves off from Aka during the Dawn.

So in other words there is no way to make a mod that adds dragon eggs and female dragons without breaking lore? That bites.

Dragon eggs? Not in the sense you mean it, not. No dragon eggs.

Female Dragons? Well, yeah, the Jills. But they don't exist except when they do, and then time does not exist so... that's rather hard to mod.

The Dwemer knew about the http://uesp.net/wiki/Lore:The_Egg_of_Time... and it was made by a Dragon, in some sense... but it's already hatched, and gave birth to a bunch of chimerical living gods, not Dragons.

Well, you could just add Dragonlings. Adjust the vanilla dragons and make 'em a bit smaller. I don't know much about dragonlings though. Not sure if they can breathe fire and stuff, since that's basically Thu'um. The Jills are a bit higher on the subgradial ladder than regular dragons. From what I've understood from Kirkbride's posts even Kyne was a Jill of a sorts.

The dragonlings can breathe fire, according to UESP, and speak Dragonish, but we don't know if it's the same language which is spoken by the Dovah. Kyne as a Jill? I didn't know it. That may be logic.

Something I've been wondering. Was Alduin a Jill? I read somewhere that Jills were black.

Nope. Alduin is an aspect of Aka, one of the multiple Time Dragons.

Well thats a bust then. I suppose if I go through with this mod then it wont be lore friendly. I may have to drop that expectation and have the quest giver admit that they dont even understand why it is happening as it goes against everything they know of the dovah.

I don't think the dragonlings are actual dragons.

High Rock is kind of a special place, all fragmented geographically, politically, socially, and so on. Perhaps Time itself was somewhat fragmented there? Maybe there really were "little Dragons" there as a natural part of the local mytho-ecology, sort of physical manifestations of the cracks in the world that exist there. But they disappeared after the Miracle of Peace? (Which would explain why later scholars couldn't find them.)

But still, no dragon eggs.

You know, it occurs to me, that if Alduin can rebel against his function, perhaps Jills could, as well? What if there actually *was* some Draconic breeding... and this was very, very bad? The quest could revolve around either destroying the eggs before they hatch into another world (and tear this one asunder)... or around somehow ejecting it from this world so it could exist separately? (Both choices could be offered.)

http://www.uesp.net/wiki/Lore:There_Be_Dragons:

I guess they're kind of like wamasu. Magical lizards sometimes referred to or mistaken for dragons, but they are really wholly natural beings.

Just because investigations of nests and such reported by peasants to the guild turned up nothing doesn't mean they never existed. I was there, before the Warp. I still remember. There were, indeed, small, fire breathing reptiles. Their build was not consistent with what I know of lizards; they looked like dragons, though of a decidedly different variety than those presently found in Skyrim. They had language. It is entirely possible that this Torhal Bjorik simply lacks information from a pre-Break timeline that others still have. It is similar to how the Tribunal Temple lacked information about events in a previously extant timeline that, while causal to the Tribunal's divinity, no longer exists... yet the Ashlanders still had the memories.

They may well not exist, not any more. Nevertheless, I have seen them.