I don't think it matters whether you fight Bowser before getting all the stars or not. As long as you have 120 stars when you defeat him, you'll get Luigi.
If you kill Moltres, you kill Molters. It will never be possible to find him again. So it's just one chance, and it's the same with the other Two and...
Nerds sometimes have difficulty with social cues, so you should make your feelings clear. That being said, give him space, too. You'll want to be direct without appearing clingy. Also,...
Of course he can! All cats come again eventually. Keep setting out food he likes and the giant cushion and he might come. Remember to check his top 3 goodies...
If he disappears for long periods of time with no explanation, then no, he doesn't value you. It may be that he's involved with other people and then gets back...
You could start training him now by getting him accustomed to having weight on his back, basically turning him into a pack-steer. But, he won't be ready to actually ride...