I think it's a very good question and also not so easy one.
I will just tell you my opinion and wait for the others opinion.
In this case, I think Korean conversation doesn't go simply as English conversation.
You say 'Thank you' and expect a proper answer 'You are welcome'.
Many textbook would teach you to say '천만예요', but it's not so common in native Korean.
I would say there is no such a formula. It depends on every different situations.
So I would choose No.4 for both of your questions.
If this is just a normal situation, I would answer as follows.
수고하셨습니다. --> 네, 감사합니다.
고생하셨어요 --> 아유, 아니에요.
감사합니다 --> 아니에요.
well, I think I am pretty much choosing No.1 now. though I just said I would choose No.4 which doesn't make sense at all. I know. but uh, this is kinda hard to explain, because not only my English proficiency is not good enough but there could be many different accents making a different nuance.
I realized this is a kind of tough question.
I will just wait for the other native Korean to answer.
Thanks for giving this question.
Happy new year^^