1. Agreed. It has to be old Jack.
2. I think shit-ninja is Riley.
3. If you ask Alyssa about his dad in ep.3 she says he left them before they born. So it is pretty obvious Alyssa and Alice are Jack's daughters. That picture you referred is the best proof.
4. "Old Jack aka Mysterious dude" said to young Jack in ep.4 April is one of his many employees. That's how she knows about Jack's time travels. And I also think Riley is another employee of Old Jack. It seems only Riley knows why that crystal is so important.
5. Isn't that obvious it is Shelby's father? He is THE villian of this AVN. I don't understand why you have no idea about this.