The first time she lets him past second base, he slowly teases her bra strap down her shoulder instead of unfastening it. He thinks maybe this way she won't feel so naked.
And he's already gone by this point. I'm very much in awe of how you shape the words, transforming them into this living breathing thing with meaning and depth. Sure, he's Puck and he's thinking about getting some, but he's also thinking about her needs, which is just so sweet that you know he has "feelings" at this point even if he's not ready to admit them to himself.

(he makes sure he's got a raincoat this time, though, because now he knows from experience that the adage "girls on top can't get knocked up" is a myth)
Ummm... YES, IT IS! Why would you ever think that was real, Puck? Geez! Love the "raincoat!" Haven't heard that one in a while.

He loves her too. He loves things about her - her eyes and her smile and the sound of her voice, too - and somehow loving a few things leads to loving every thing.
AND BOOM! Epic Puck revelation moment! Yes, loving certain things can lead to loving the whole. It's scary but it happens.

The words slip out as if by their own accord, small and soft and sudden. He doesn't even realize it until Rachel bristles and pulls away for a moment.
So like Puck to just not be in control over the situation at all, and thinking automatically that it's the biggest fuck up ever.

Then their conversation. I'd quote the entire thing back to you because of what's said and what's omitted. She doesn't say it back to him and that's okay. It's enough to know that she believes him when he says it to her. Enough to know that he's willing to be honest with her (which is something he's lacked in all other relationship - friendly and otherwise - up 'til now.

This was really masterfully written. Great job.