Your rephrased sentence is grammatically correct and does make the structure look clearer.
However, moving “though” changes the nuance slightly.
In the original version, “though” contrasts the first clause (reputation being tarnished) with the second (emerging unscathed).
By placing “though” later, the emphasis shifts and the sentence takes on a different meaning.
The original version aligns more naturally with the intended contrast.
For Q4:
You’re spot on that “make” connects the first idea to the third, keeping the sentence coherent. Regarding commas, the rule does apply here. The phrase “which often find great merit in otherwise ________ literary gems” is non-essential—it adds detail about the reviews but doesn’t change the core meaning of the sentence. That’s why it’s set off with commas.
So to make the sentence structure clearer, you can read the sentence without that part