If you do not have any existing resources, can you delete the CRDs and then re-apply? Or if you do, what ECK version are you upgrading from and what version of kubernetes/kubectl are you using? That error where it is rejecting the Kibana CRD is new to me at least.
the download suggests 1.0.1 for the operator but the file contains v1beta1
This is expected as the 1.0.1 CRDs include v1beta1 in the versions list for backwards compatibility.