First off, check to make sure nothing had fallen inside those 2 sockets that could cause a short.

After that, look for pinched wiring.

Just curious. I have an EBD and have been thinking of doing the very same thing. How long and how difficult was it to strip the playfield and put it all back together?

As for your problem I agree with indypinhead. Also look for leaf switches that could be broken and the wire dangling. Anything that is out of pace. Pull on wires where the solder to connections to see if they are solid. Get another person to look at it with you. Two weeks ago I have my slings, bumpers and everything in the column in that switch matrix stop working. I looked all over and could not find a short. Started looking into the board. I tested with a signal from the board pin all the way out to every switch and got signal. Tested all the switch diodes. Everything tested good. Had a friend come over and look at it with me. He noticed almost right off one of the 30pt switches around the bumpers was broken off with the wire still attached and It was laying on another switch. Taped it off and it started working properly, minus the 30 point switch. Point is lots of times after you've looked and looked and can't find it a new set of eyes often can see it. Its there its just a matter of finding it. Use your tested and test for continuity by plugging the board to the harness. Put one of your tester probes to the pin on the back of the plug on the pin in question and the other end out to the switch in question. Continuity yes then try it at other points nearby under the playfield and see if you're getting continuity elsewhere via a short. Just an idea. Good luck and don't rip your hair out.