PayPal normally sends the buyer a receipt email for their payment, but if you need to provide a more detailed invoice, this help page explains how to customize your E-junkie-generated thank-you pages in the format of an invoice:
http://www.e-junkie.com/ej/tips.thankyou-page.invoice.htm
Aside from that, we could only suggest using our custom/third-party Integration feature to have us submit the order details to a custom script at your end that could do whatever you wish with that data, such as assembling it into an invoice, with whatever custom invoice numbering you may require, that would be emailed to the buyer:
http://www.e-junkie.com/ej/help.integration.htm
If you'd need some help setting that up, we can recommend the competent, E-junkie-experienced developers for hire listed at the "developer directory" link you'll find at the top of our site.