Wrap up codes only exist for queue calls at this time, as the wrap up codes come from the queue itself. You could manually add a disposition to the activity record within Salesforce, but there isn't a way to "pop" the after call work/wrapup code window within the client for non-acd interactions.
For the call log association, is it possible that you don't have auto association set in the call center definition (note that classic and lightning utilize separate call center definition files)?