When do you put in the peppers and parsley?

I would add half the parsley and crumbled chili just before I add the tomatoes. I would add the other half of the parsley at the end when tossing the sauce with the pasta

Just to be the voice of discontent, I don't care for raw parsley. I agree with the peppers, but I would add the parsley while tossing the pasta with the sauce.

This is why there are so many versions of even ancient recipes.

Parsley for is always a finishing herb, mixed in as the last ingredient. The chilli peppers I'd crumble and add as the tomato reduces, being ready to add more as time goes on. Sometimes the heat dissipates with cooking, sometimes not. So taste taste taste.