Ok looking at the schematics, 1 on each of the displays is segment 'h'. This is a different segment then all other numbers. Segment 'h' on player 1 to 4 is driven by gates on Z16' pins 10 and 12.  I would be fairly certain this is your fault, replace Z16 it is a 7404.

The reason the 1 works on the credit display is that segment 'h' on this display is driven by Z17.

This should fix it. If not it may be U5 the 40 pin 6532 display control, but I doubt it. Replace Z16 and report back.

You could also check pins 8 and 16 of A1 J2 but I doubt they would both be faulty. Pin 8 drives seg h for 1st and 2nd player and 16 for 3rd and 4th

After looking at the schematic and confirming your description I removed Z17 and Z16 and tested them both in my programmer / ic tester and you are spot on Z17 tests ok and Z16 tests faulty. 
I only removed Z17 to prove my IC tester was working properly.
I still have to prove it in the pinball machine but I'm 100% it will work

Now to find out which display killed it.
First it was only player 3 and 4 that was missing the "1" but after swapping one of the displays from player 3 to player 1 i also lost the 1 on player 1 and 2 even though the displays were swapped back.

Thanks for your help, saved me some time and it may help someone else in the future.