Well, you're on the right track with different ISBNs. It sounds like you're doing what would be considered a revised edition, as long as it's substantially the same work, just with some modifications.
The revised print edition should have a new ISBN so that readers know there's a substantial difference from the original. When you self publish the new edition on KDP, there are items to answer about what edition this new book is (revised, 2nd edition, 3rd edition, etc.). KDP will assign a new ISBN for your revised print edition when you publish it.
As you're probably aware, a Kindle eBook is automatically assigned an Amazon ASIN number. As with the revised print edition, when you self publish the revised eBook edition on KDP, a new ASIN will be assigned. You can add an optional ISBN, but that will be a cost for the number that you'd purchase through Bowker (if you're in the U.S.).