Hello Matt,
Many thanks for your interest in Hauptwerk. Have a look at the Custom Organ Design Module user guide at http://www.hauptwerk.com/documentation. You can use the example CODM files included with Hauptwerk for reference as well as use the St. Anne's organ samples to learn about formatting files in the proper format for use with Haupwerk.
Hauptwerk uses standard .wav files so you should be able port your files, licensing allowing.
We aren't able to provide full support for creating sample sets, however you should be able to learn the process by examining the CODM guide and files as well as other users posts here on the forum under the CODM forum.
I hope that helps.