Quoted from egg_sanwich:
In my (brief) experience working on these EMs so far, I find it usually best and advisable to pick one problem to focus on and go from there.
Here are a few quick thoughts since I've been working on a Pro Football recently as well.
The flippers are dead during game play as well? Try checking the Q relay, there is a normally closed switch that must be closed for the right flippers to fire. However the ball shooter coil does not require this closed switch, hence why it can still launch the ball.
Check the normally closed switch on the AB relay. Mine was not making solid contact so would sporadically do this as well. This switch must be closed for the P, O and ball count unit relays to fire, although poor contact seems to have caused it to fire twice in some instances.
Q relay also plays a role in the ball counting sequence, and it seems that a few other issues might be hinting towards this relay as well.
How are you manually adding games, via the coin chute switch? How is your free play set, by closing the switches on the credit reel? Can you elaborate on "not start regularly"? Might be worth investigating the startup sequence to see where you might be going wrong here.
This is normal, the pop bumpers are only lit occasionally during game play, and scoring the 1000 points will unlight them. I think it is on a kind of alternating relay that controls this.
Do you have the schematics for this game? Getting a copy of the schematics as well as instructions with the startup sequence listed has proven invaluable for me in troubleshooting my Pro Football, and easily worth the investment.
EDIT: rereading this a bit, it sounds like the Q relay is a great place to start.