Don't worry about the GI voltage. You cannot accurately measure that circuit from the fuse to ground. The fact that your GI is lighting up means you don't have issues there and that circuit does not impact the 5V supply.
Next in line is 4A fuse F5 on the power supply board. It is the fuse closest to the right on the power supply board. You will see C15 to the right of it (very large capacitor). Check this fuse is good.
Set your meter to DC and measure the voltage on C15. Negative lead of C15 is on the top, positive on the bottom. Should be 10-12V.
NOTE: Be careful when working on a power supply board that is powered up. The components on the left of this board power the plasma displays and is 100V and is dangerous. Never touch any of these components when the game is on.
Also, check that you have the boards mounted with screws and they are snug. These screws participate in keeping the ground level consistent between boards.