1. When does the game end? The rules say things like "when the game ends", and imply that the decks time the game end, but I don't see where it says the game-end trigger.
Note the turn order track on the main board. When everyone has exhausted all actions, that ends the turn and the track is advanced. The game ends at the end of the final turn noted on the track for your number of players/game chosen.
2. Venture Capital-- is there any negative effect to it at the end of the game? Or is it just bonus VPs for the person who borrows the least?
No penalty; just bonus VPs for least number of cubes in the VC area.
3. The rules governing Private Contracts seem to contradict themselves:
The Rules wrote:
At the end of turn 3, before turning over the replacement contracts, discard the A private companies deck and use the B private contracts deck.
All private contracts are drawn at some point during the course of the game.
What's the deal? Was the first bolded portion supposed to not be there & this actually happen at the end of turn 4?
Hrm. This looks like an artifact that slipped through. As there are only 12 cards in the A-Private deck, and you reveal 4 per turn, the A-deck will be exhausted during the set-up for round three. You'll have no cards left to discard (and all will be used during the game:
Set-up: reveal 4 A cards
End of turn 1: reveal 4 A cards
End of turn 2: reveal 4 A cards (deck exhausted)
End of turn 3: reveal 5 B cards
End of turn 4: reveal 5 B cards
End of turn 5: reveal 5 B cards (deck exhausted)
I hope that helps!