Welcome to Pinside, and congrats on getting a Sky Line, that is a great game!
At the start of a new game, the ball gate is supposed to stay energized until you score some points, so for the moment I would not worry about that.
The score motor running sounds like you are not coming out of reset. The most common reason this happens is because the game is waiting for all of the score units to return to zero. Since you have two score units that are not working, you should check to see if this is your problem. On the control bank (the long row of relays mounted on the bottom board) look for a relay marked RESET COMPLETED or something like that. If this relay has not tripped even though all the score units are back at zero, try tripping it by hand to see if that makes the game come out of reset. If so, then the circuit that is supposed to detect that all score units are back at zero (which would trip the RESET COMPLETED relay) is not working right.
Do you have a schematic for your game? If not, you really should get one. The Pinball Resource sells them.
- TimMe