When you say "the 1,000 point reel won't always roll over", are you saying that it goes back to zero without incrementing the next higher reel? The most likely candidate for that type of problem would be 9-position switch not working correctly on that reel. Take a look at that switch and compare it to the other (working reels).
What happens with the ball drains? It should score the 1-10 bonus unit (the rollover pins that are currently "down" score 1,000 each) and then it should score the strike bonus unit 0, 2, 4, or 6 times if you have 0, 1, 2, or 3 strikes respectively.
When you trigger an extra ball, the red star lights up, right? What should happen is that after the ball drains and the bonus scores, the extra ball relay should open, the red star will turn off, and the ball will get pushed to the shooter lane. Is the red star still lit when the ball goes to the shooter lane?
I'm not certain about score cards because I've never change that setting and my Triple Strike is set to extra ball mode with extra ball at 85,000.