OK, so a couple of things:
1. There is no "Stage 2" for the inning programs. The stage 1 is all there is. I know there is that template text for them, but they haven't been used yet for the innings programs. You aren't missing anything there. There ARE multiple stages for Team Affinity and some of the player programs that you can unlock once you complete Stage 1.
2. As others have stated, you're pretty much screwed on completing the 300 stars for the bosses for older Innings programs. Now, the good news is that most of those cards are more or less obsolete. However, if there IS a particular player you want, you can accrue the stubs to purchase the card off the market. Why they did it this way this year (and last) is beyond me.