You probably also have some cracked solder joints on the connectors. It would be worth reflowing the connections to the header pins for any connector you think may be a problem.

Be careful if you remove the entire backboard/hand assembly. There are two connectors that are identical for some inexplicable reason. If you plug them in backwards you will take out at least one of the chips in the switch matrix. Not a terribly hard thing to fix but a pain in the ass that can be avoided. Ask me how I know...

Not sure what you mean by Jones plugs but two kinda squarish connectors... maybe 9 or 12 pin with thin wires to the matrix. As long as you marked them uniquely you should be fine. Hard to believe that I couldn't find this mentioned anywhere after I fried my game putting it back together, so hopefully this helps get the word out.