Just like when you're ironing out a purchase price, the post-inspection period is about *negotiating*. The seller makes an initial request, you respond and then you go back and forth until you reach an agreeable point or you go your separate ways because you can't.
However, if we're talking $1,000, I'd just fix what they're asking for unless it's something ridiculous like asking you to fill nail holes in the wall or something. Would you really want to risk them walking away and having to start all over again with a new buyer for $1,000 - especially when you're going to have to tell that buyer from the get-go about these issues now that you know about them?
Put yourself in their shoes: How would YOU feel about buying a house with a leaky roof?