As someone who has been on the receiving end of potential fraud twice, I would make 2 points. Firstly, that last email from Paypal means that they recognised the fraud before you had contected then, so, whilst in theory, you are still liable, you should find them totally on your side. Quite how this occurred you will probably never know, but I wonder if you received an unexpected communication from an Ebay customer and used the reply facility in the communication. If ever you do get any form of enquiry, do not reply. Log on to My Ebay directly, and answer from there.
The second point to make is that, you should pay all your bill apart from the fraudulent amount. Then, when all the matters are safely resolved, you will be in a much beeter position to argue that all the interest and other chanrge should be refunded. In any case, you always have at least 3 weeks bewtween the transaction date and the date you have to pay your bill - meanwhile keep up the communication with both Paypal (to make sure they are resolving the problem) and the Credit Card company (so they are fully aware of what is going on). Try to get a case reference from your CCC and then you could also copy any relevant emails from or to Paypal to them.