Hello Ex-jobb
One important thing about the example I created, is that the routing of the CLK signal has to be done board-wise, not port-wise. If you have a (unsorted) list of CAN ports you need to find out first which of those handles are for ports on different boards. You can use the ncGetAttr.vi (SerialNumber) function to figure out programmatically, whether two interfaces are of the same board or not (see attached screenshot). You just need to perform the 'connects' on the list of handles that contain ports from different boards (half as many handles).
Regarding the Mask and Comparator settings: As you are using Series 2 CAN hardware, you might want to use the Series 2 Filter settings rather than the fields of the configuration cluster. For more information on the Series 2 filters, see the corresponding section in the online help (CTRL+H) for the ncSetAttr.vi
Regards,
-B2k