There is a way easier method of tieing the grounds together.
See: http://www.pinwiki.com/wiki/index.php?title=Gottlieb_System_80#Ground_Improvements_for_System_80B_at_the_Transformer_Panel_-_.22Tag_Team_Pinball.22_to_.22Spring_Break.22
The article is from the PinWiki 80B section but applies to System 3 also.
Like WhiteStar driver boards that use FETs, there are tiny connections that must be in place for the part to operate correctly. When not in place, one side effect is for the FET to switch on once and stay locked on.
Post pics of the front/back of the board. Let's have a look.
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Chris Hibler - CARGPB #31
http://ChrisHiblerPinball.com/contact
http://www.PinWiki.com - The Place to go for Pinball Repair Info