For #1, think about the flow of the entire passage. Pay close attention to the action of "direction words," words that serve to direct the flow of an argument, either by adding on and amplifying, or by creating a change in direction by a contrast word.

Although many lines of evidence indicate that birds evolved from ground-dwelling theropod dinosaurs, some scientists remain unconvinced.
Ambiguous opening sentence, typical of academic writing--the author has not yet shown his hand, what he believes.

They [the unconvinced scientists] argue that ....
so far, we don't know what the author really thinks . . .

BUT investigators have now uncovered
Ah ha! That word "but" is HUGE! This is a very classic argument format: "My opponent thinks X, BUT I think Y" This is a very effective strategy in argument, because the implication is that I know & understand my opponent's argument but I know better.

The next sentence "in any case," which is a way of adding on an additional point. This strengthens his response to the first objection.

Now, another round:
Skeptics also argue . . .
Again, the author is stating the opinions of those with whom he disagrees, more objections.

This objection was reasonable when . . . but . . .
Rhetorically very effective: he gives a partial concession to the opponents view--yes, it worked in the past, but it's nonsense to believe it now!

"Finally" = another strong summary word.

Throughout the whole passage, the author was stating the objections to the theory and then was arguing against those objections. He was defending the theory that "birds evolved from ground-dwelling theropod dinosaurs." Anything that states the meaning of the paragraph should capture this back-and-forth, objection and then response to objection, which happens a few times. The author is not simply evaluating, which implies a neutral agenda. The author has constructed sophisticated argumentative structures to respond to objections. Thus, the best answer to #1 is
(E) respond to criticisms of the theory that birds evolved from ground-dwelling theropod dinosaurs

For #2, look at that section of the text:
They [the unconvinced scientists] argue that theropods appeared too late to have given rise to birds, noting that Archaeopteryx lithographica—the oldest known bird—appears in the fossil record about 150 million years ago, whereas the fossil remains of various nonavian maniraptor theropods—the closest known relatives of birds—date only to about 115 million years ago.
This is objection #1: birds are old, 150M years old, and nonavian maniraptor theropods are not that old.

But investigators have now uncovered bones that evidently belong to nonavian maniraptors dating to the time of Archaeopteryx.
First, specific response to objection #1

In any case, failure to find fossils of a predicted kind does not rule out their existence in an undiscovered deposit.
More general response to the objection.

Let's think about the author. The author is defending the theory that "birds evolved from ground-dwelling theropod dinosaurs." Obviously, what would strength his case the most is if scientist found definitive evidence of ground-dwelling theropod dinosaurs from the time of the first birds (150 MYA) or older. Short of that, he argues that the current absence of these are simply due to the fact that we haven't discovered them yet. The particular fossils that interest him are "ground-dwelling theropod" as old as birds (150 MYA) or older.

The best answer is
(C) Theropod fossils dating back more than 150 million years