This is probably the most grammatically correct, and it's what I'd write in a formal essay, etc. but it's not very colloquial.
In a formal paper, you might write, "After having explained the methodology, I will now move on to the results". That is the correct use.
"After showing you the paper today, I will give you some notes."
This is understandable in the context, and you could use it. But you'll notice that it could refer to a lecture that you haven't given yet (if you leave out the "now").
The problem with your original:
"Here are just a few notes after showing the paper today".
is that "showing" has no subject. Grammatically, it seems that the notes are the thing that showed the paper.
So, the closest colloquial expression might be:
"After showing you the paper today, I'm now going to give you a few notes, "
But, you're right. In formal use, you'd use "after having shown."
Student or Learner