pin 9 on U8 is for the "dot" on display 2.

Connector J3 is split into 2 halves, pin 1 is ground, pin 2 is 5V logic, then pins 3 - 10 are all for display 2 - the rest 11 - 26 are for display 1.

The buffer chips have all been replaced, but, you say you put 4049 in there??

Schematic has them listed as 4050 which is non inverting - the 4049 is an inverter,
schematics clearly show these as definately non inverting, both listed and on diagram.

...I printed off the diagram for your machine as this part differs to my space station

Also do you have signal going into J3? - follow it back through connections. You have lost signals from somewhere either at this connector or before it. BUT, once you get the signal back, if the right chip is not on place at U8 etc, then all youll get is garbage displayed

I initially bought 4050's (as per other thread), however on the board they were actually 4049's (original).  Clay has a note on his site with a disclaimer that the schematics have errors in relation to these..I checked the manual for the display board parts and it has them listed as 4049's.

I cant have the machine in a powered state at the moment until I put the new bumper lights in (exposed wires under playfield) and the last thing I want to do is kill the cpu board with a short!  I have it in front of me in front of computer with DMM trying to get as much done as possible.  IF the PinScore LED's work perfectly (then I can not worry about SRC's on CPU) and actually play and enjoy the game.  I'm just trying to get this working (a) for the challenge and to learn (b) get the damm thing working!

I've been though Clay's guide all day (finished doing U12 & U11) and it cleaned up real nice.  Previously I was not getting readings anywhere near what Clay suggets but now - all but U16 are looking good..

If there is not much else I can do on the bench, I will wait until I get the lamps done next week (when parts arrive) and will attack it again then with your advice!