I didn't discover the show and PJo until about 2008, so I already knew they were going to be together because it already aired. That's an interesting experience because I already knew they would go there so I did see their earlier scenes through that lens.
And I agree, after like episode 3, I'd say, Pacey kinda forgot about his deal with Dawson and just wanted to hang out with her. I mean after episode 2 and their talk in the car, I feel like it was already changing for Pacey, but then when she defended him from Dawson of all people and stayed by his side instead of Dawson, and then their meaningful talk at the marina, that's when it really changed for Pacey into just wanting to be around her and hang out with her.
I mean, just his look here after she says "when it's right" and that's her basically saying that he shouldn't believe the "general consensus" about himself, and I think that meant a lot to him.
And then their look at the end of the episode too. And then the line with Dawson about "if they're gonna beat each other up, it should at least be over a chick" which is the biggest foreshadowing lol
And what's funny is that Dawson asksed Pacey to look after her for the next "couple of days" he never said weeks or months. It was Pacey who continued to hang out with her when he could have just said "see ya" and stopped hanging out with her.
And we know that while Joey didn't have any sort of deal to hang out with Pacey, she was reluctant to at first, but episode 3 changed things for her as well. Like hshapir2 says, Joey chooses to hang out with Pacey in 304 instead of turning him down and doing something else.