Cool, chris91!
I assume you are talking about Gottlieb's System 1, since I believe Recel went straight to "System 3" for unknown reasons. It would be interesting to know the name of the game you are reviving.
For most functions, I found it much easier to repair (where needed) the existing boards, rather than making new. However, some areas of the Driver/Multiplexer Board of my Crazy Race machine was so burnt that I let Arduino handle the multiplexing and made a new Lamp Driver "Add-On" Board for the bonus lamps.
But I repaired the control board for the 7 segment displays by replacing 2 fried 7475's and then I imitated the signals from the totally destroyed CPU Board, step by step just like you. To generate a refresh frequency matching my machine, I inserted a 150 microseconds delay before each strobe (two digits displayed at each strobe) and then activated for 700 microseconds:
delayMicroseconds(150);
digitalWrite(X[i_strobe], HIGH);
delayMicroseconds(700);
digitalWrite(X[i_strobe], LOW);
Please note that if you have another system, you probably will have to use different delays. Also note that my approach requires two Arduinos; one for the playfield and one dedicated to control the top box.
I put 1N4148 diodes between the Arduino and solenoid drivers, just in case one of the driver transistors would break down and short, and send 40 volts back to the output pins of the Arduino. I don't know if this will help, but at least it makes me feel a bit better.

Good luck with your project, chris91! Please let me know of its progress.