As per my experience with passport, it is working fine till date. Have not faced any issue. Would love to hear more about the problem that you are facing with passport. What IDE you are using for debugging.
If you are working on small project then I would recommend you going with passport. As you will only have to worry about you business logic over user management.
But yeah, if you are working on big project and you have time to re-implement the login wheel then you should implement everything from scratch. In this case you will have to manage sessions and all that stuff with passport handles.
As you mentioned that you need help with JWT tokens. Check out this link, this guy explains everything you need to know about JWT.