The mock offer he made to Lily is not funny. It's the kind of kick the dog thing authors write when they want to make you dislike the villain. Eliezer is better than that. What made it laughworthy for Voldemort was the delicious irony of Lily offering her life in exchange of a life that would not have been taken to begin with. From this it was clear he knew the whole prophecy and that Snape heard the whole thing. Took me some time to figure out why it's different from canon, though of course that should have been clear too. Snape is no fool. And the outcome of his no-fool-ness has been known by than.
About your list, I think the failed-notice thing in ch 3 is simply the 'strikes directly at the soul' and 'leaving only the burnt hulk of his body' thing. Also I doubt Voldemort would share his plans with Lucius.
But, yeah, plenty of clues.
(And somewhere in the back of his mind was a small, small note of confusion, a sense of something wrong about that story; and it should have been a part of Harry's art to notice that tiny note, but he was distracted. For it is a sad rule that whenever you are most in need of your art as a rationalist, that is when you are most likely to forget it.)
Why does the wizarding world believe Voldemort used the Killing Curse on Harry? Whether or not the Love Shield exists in MoR, I doubt most wizards had an >epsilon prior for the Killing Curse resulting in a scarred but otherwise unharmed target, a dead and burned spellcaster, and a destroyed building. There were no surviving witnesses except Baby Harry. Where did that version of events come from?
If I was Joe Random Wizard and heard that evidence without names attached, I would naively hypothesize: Dark Wizard shows up at house, encounters mother + father + their allies. Battle ensues. Parents and Dark Wizard are slain. House is destroyed and baby is hit by debris. There is one obvious question - why the allies didn't take the baby with them - but any answer to that is more plausible than "There were no allies; the most reliable curse in the world backfired on its most experienced practitioner."
Not that the "reflected curse" story was hard to sell. People are great at not asking the next question when they want to believe.
We have some additional information about the events of that evening:
What really happened at Godric's Hollow?
PS. If the Love Shield does exist in MoR, do you suppose Bellatrix could cast it?