Hi @NKolenberg
You are right that the funnel report can not be built using custom data properties. Your custom data properties are limiting which contacts are included in the report, but not where in the report they are shown - which is still based on the standard ‘became a’ properties.
One option is to change your funnel report so that it shows contacts that Any strage in the report, rather than All, so that contacts that missed lifecycle stages are still shown. If this doesn’t help, then the funnel report may not be an option in this instance and more numerical reporting may be the best you can do.
Hope this helps, Phil.