Have a look at the Hauptwerk v3 ExampleCustomOrgan2.CustomOrgan.Hauptwerk.xml and ExampleCustomOrgan6-StAnnes-WithAllFrills.CustomOrgan.Hauptwerk.xml files for examples of how to use action noises. Basically you just need to cheat by telling Hauptwerk that the files are tuned to A- 440/equal at a given rank pitch (e.g. 8') and tell it to play them back at that rank pitch (e.g. 8'). Then no real-time re-pitching will occur.
See also the section on action noises in the CODM user's guide.
You might also need to rename the files to the CODM filename format (036-C.wav etc.). First copy them into an 800000-899999 range installation package of your own if you want to edit/rename them.
At the moment there seems not to be an associated InstallationPackageDefinition file associated with these.
That's not actually possible - a sample can only be referenced via an installation package (See the Sample table in full-format ODF). However, they don't necessarily have to be listed in the package definition file (not a strict requirement for CODM use).