I can understand there being a delay in emails received... (Of course that should be worked on. Customers should not be receiving "Pay now" emails well after the actual payment.)
But the wording... it seems offensive. "It's all yours, now you just need to pay". Wrong, wrong, wrong. Perhaps Americans don't realise that "It's all yours" is also used in a dismissive & offended way in Australia, as the following example illustrates:
Ferdinand: "Look, will you just get out of my way while I finish working on this cupboard?"
Barbarella: (offended, throwing down her powertool with manicured hands and emitting a carefully coiffed sniff) "Oh. Of course. It's all yours. You can do the lot."
People say "It's all yours" in a variety of circumstances. It can be said when giving a gift to someone, or when selling something to someone, but the "all" is actually not standard in Australian speech. We might say, "It's yours"... but people say "It's all yours" to imply they are backing out of a field or situation in which their expertise or help is not valued.
To follow that up with "Now you just need to pay" compounds the feeling of wrongness. It seems to be trying to be jocular and "matey", but it is very far off the mark!
The following might be better:
It's yours - your eBay bid/purchase was successful.
Hi [name],
We hope you enjoy your latest purchase. Please arrange payment now, and your item can be sent once payment is complete.
(If you've already made your payment, please disregard this email.)
You can pay using the following methods: PayPal, bank deposit, cash upon pickup. This would of course be different for each seller, depending upon the payment methods accepted.