From your description, it seems like the hole circuit is working properly:

utsnitt_1 (resized).jpg

But if the score motor continues to run because something else is stuck and prevents it from stopping , it will repeat the hole kicker sequence over and over again. This may also explain why it keeps on adding 1000 points, if the ball count unit does not advance and keeps the ball index relay energized. (If I remember correctly, every game starts with a bonus of 1000, added at the start of the reset cycle.)

utsnitt_2 (resized).jpg

Is the ball count unit stepping up and down correctly?

The score motor should be in position 0:

utsnitt_3 (resized).jpg

The black dots only indicate where in the sequence the switches on the numbered stacks changes state.

I.e. all "SCM 1" switches will be in the opposite state of what the diagram says in all other positions than 0. More info here: http://www.pinrepair.com/em/index3.htm#motor