Ummm... Dude, in all honesty. Who cares? Yes, it was a joke, a bad one at that. But the whole point I'm making is that rep isn't everything. And no, I wasn't the one who gave you bad rep. I've never given anyone bad rep on here. Besides, this thread isn't about you and the bad rep you recieved. It's about giving advice to John.
As for John... Just saying something like "Do you want to hang out sometime?" Or plain and simply "Do you want to go out sometime?" Most chicks will see no difference between the two anyway. And see what she says. If she says no, ask her why... Then move on. Plenty more fish in the sea, as the saying goes.
I've been through this phase myself many times, so I'm speaking from personal experience here. Don't know how many times I've heard the line "I think it's best we just be friends." And yes, it does annoy you sometimes, but you learn to live with it.
That's about all the advice I can give. Hope it helped.