Selling elearning to client with LMS

2. and 4. are very close, and important. To start with, the .story file is the actual valuable part of what you are selling. It is the original. If they have the published then zipped form, they can upload that and it will run on their LMS. The key is to agree with them before you start as to what you will give them. If they only get the zipped result, they are, (in my opinion) foolish. They can't modify anything without you (or whoever possesses the .story file.) They may bargain to pay less not to get the original, but again, that's penny wise and pound foolish.

Part of the consideration for what is delivered is who owns the copyright. The answer to that is the answer to who gets the .story file. I, personally can't imagine creating something for someone, and not giving them everything. Especially if they commission a specific work, it would be difficult legally, and as a matter of negotiation to take the copyright from them. If they do own the copyright, not giving them the .story file is stealing their asset.

On the other hand, If you have a set curriculum that you created and you sell the usage of it to a variety of clients, then you have the copyright. and they are paying for the right to make and use a copy. You own the copyright, and you keep the original. In that case, it should come to them at a significantly cheaper price.

Of course, this is all my opinion, and not legal advice. If there weren't differing legal viewpoints, attorneys would be out of work. You might check with one, if you want the real legal scoop.