I think I got off track here a little bit as your were asking for help for strobing GI's. For your 5V section you are loosing .2V between the MPU and PDB, this is going to be caused by headers/connectors and is one of the primary caused of your original reset issues. The 5V is also starting off low, replacing the 5V regulator would likely correct this, but for now your reset fix is working, just keep this at the back of your mind if you experience additional issues with resets.
For your
Quoted from jesperpark:Now it booted back up, it did restart once in 5 minutes but I was able to play 2 games. Issue now is when i hit start, the 6 bulbs for the shields start to flicker. I then left it on for another 10 minutes with no more restarts, but all the LEDs are really flickering across the whole machine. So I am guessing it's something bigger and looking for advise what to start looking at next.
Is it just GI's that flicker, or is it all lamps in the game? If its just the GI's then I would suspect an issue with the dimming circuit or control data. There is a couple of easy things you can try...
Flip over the ribbon cable between the MPU and PDB, this will make change the conductors used for communications.
Go into game settings and disable the GI dimming feature, if the problem persists, the issue is likely on the PDB itself.
Pull the MPU, place on a hard flat surface and press in on the ASIC chip to ensure its seated well.
General dimming "theory of operation"... from PinWIKI http://www.pinwiki.com/wiki/index.php?title=Williams_WPC#GI_Lamps_Not_Dimming
The driver board generates the ZC signal with the BR2, D3/D38 and U6 circuitry (different resistors).
The ZC signal is connected to the ASIC (across the driver board, the ribbon, and then across the MPU).
The ASIC uses the ZC signal to determine when to send the /TRIAC signal to U1 pin 11 (an 74LS374 buffer IC) as it simultaneously presents GI string enable data on the data bus.
U1 latches GI string enable data from the MPU's data bus.
The output of U1 forms signals T0 thru T4, which enable the TRIAC circuitry.