Information on actually editing the template file can be found here:
http://gbatemp.net/threads/how-to-editing-online-header-template-file.377314/
It looks a little daunting, but all you really need to do is dump a game (preferably one you purchased new and still own), extract the header information using the Gateway ROM Patcher, and open the resulting .bin in a hex editor.
Using the information in that thread, the header string should be easy to identify, and you have all of the information you need on changing the chip ID per game if necessary.
Of course it's still not confirmed whether this is the reason for the bans, so private headers may not do anything. But it's still a good idea since it's the easiest way Nintendo could identify illegitimate copies.