PHP version can be found on the version link on the admin panel. (I made an assumption that the looking into it statement was related to the upgrade, but could have been in reference to finding the PHP version.)

So your store is basically ZC 1.3.9d with the two paypal payment methods and whatever shipping methods that come with the store, but there was no other code installed to the site, no image handler, no commercial shipping method, USPS isn't used?

The two failed purchases, were they through PayPal Website Payment Pro only?

Have you followed up with the customers to try to determine if there is something consistent about the two orders?