For ClickBank, bear in mind that you will first need to setup your product as a ClickBank-only product (as if you weren't using E-junkie at all), which means you would initially need to setup the product with a temporary thank-you/download page on your own Web site. After ClickBank approves the product, then you can add it in E-junkie and edit your ClickBank settings to use the E-junkie thank-you/download page:
Within 15 minutes after you upload a file, we should have your file synched up to our Amazon S3 provisions, which is about as high-performance a download service as can be had anywhere. Bear in mind that any download can only be as fast as the slowest link in the chain, which is usually the downloader's own ISP connection.
Yes, we do add a randomly-generated authoring password when we stamp your PDF for each buyer; for security, we cannot disclose the length or character set used for that password, but rest assured it is VERY long.
We haven't seen any problems with stamped PDFs being viewable in Apple Preview, and one of our tech support people uses a Mac as his main computer, so apparently there is something odd about your original PDF causing the problem. If that Adobe online PDF creator you mentioned doesn't work for you, try searching for "free PDF optimizer" to see if there's a Web upload service that can shrink the size of your PDF and "flatten" any layers that might be in it (what you described sounds like some sort of layering jumble).
Feel free to send a copy of your original file along with a stamped copy you can't view properly in Preview to our email listed here: