Unfortunately the stack trace does not contain a proper error message - only the technical details that would normally follow after the error message. As such it is hard to tell what went wrong and is preventing you from deleting the model.
Depending on what you modelled in the custom model and how it was used, it may be hard to impossible to eliminate all usages of it on existing nodes. E.g. if you modelled types, you'd need to delete all nodes using any of the types, including versions and elements in the trash can (which you already mentioned you cleaned). If you modelled aspects, it may be way harder to identify what needs to be deleted, because those aspects could be present on any node, or may even be in (old) versions of nodes instead of the current state, making it that much harder to find.
In general I always recommend to not use the Share Content Model Manager outside of a development or test environment that you can re-initialise from scratch without much effort. That feature is just not suitable for long-term use / management of content models.