Right away we know that there are two solutions for each crossword. If we look through the clues, we can see a pattern: in every puzzle, both clues with question marks cross each other in the middle square. This gives us a hint that only the middle square of each puzzle changes from one solution to the other.
The next step is to solve the crosswords. Each of the clues with a question mark is referencing two possible words. For the first, we have COMIC/CONIC crossing with DAMES/DANES.
Second, we have PARES/PAVES crossing TORAH/TOVAH.
And finally, FLIES/FLEES crossing SHILL/SHELL.
For extraction, look at the corners of each puzzle. Notice that they make up a ROYGBP rainbow. Write out this rainbow as a word; the last step is to figure out which letter goes where. To do so: in each puzzle the top-left corner has an A and bottom-right has a Z. These stand for the earliest and latest alphabetically of the two center letters, respectively. For puzzle 1, M goes in green and N goes in purple; repeating this for each puzzle and ordering letters in rainbow order gives us the answer VERMIN.