Usually there is a connector which goes between the CPU and the Driver board. If you have 5 volts at the driver board you may have less going to the CPU causing the reset. I had a similar problem with my BSD where it would randomly reset. It was the connector going to the CPU that went bad. You can measure the voltage at the Capitol on the CPU. If you have less than 5 volts there the connector is the problem.
Recheck the connectors between the 2.
Are the wires in the right place? Maybe a wire got switched if you replaced the connectors in that area. Check the connector to the CPU and replace that.
A good source is the pinball ninja website. You have to donate $20 but the owner has these problems documented and can help.

I would check the connectors between the CPU and the driver board. I bet you are losing voltage through the connectors. Look at 4.8.9 on PinWiki or Repair 753 on PinballNinja site on how to test and fix the problem.
I was having reset issues on my BSD and it had to do with the connectors between the CPU/driver board. Even a slight drop in the 5 volts will cause the CPU watch dog chip to reset the game.

Not sure if you fixed this but this is what I was talking about:

http://pinside.com/pinball/forum/topic/fish-tales-intermittant-reset#post-1532602