If you don't have significant experience repairing boards with delicate traces, you should strongly consider sending it to a pro.
What you are seeing is most likely flux residue. Since you've already identified pulled traces, the job will be a bit tougher than normal. I absolutely love this reproduction board from GPE...
http://www.greatplainselectronics.com/proddetail.asp?prod=140-101
The reason I like it is that you can solder two quality machine pin sockets into the U2/U3 position while attached to the repro board. This ensures that the pins line up. The repro board is engineered to include redundent connections between all of the pins possible. Awesome product.
If you want the board repaired professionally, I can take care of that for you. I've done dozens of these, along with just about any other pinball circuit board. Send a PM if you'd like me to help.
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Chris Hibler - CARGPB #31
http://www.Team-EM.com
http://webpages.charter.net/chibler/Pinball/index.htm
http://www.PinWiki.com - The new place for pinball repair info