It's really hard to repair an EM like this. my suggestion is to go through the entire game. all these things are interdependent. see http://pinrepair.com/em/index1.htm
Everytime i try and fix an EM like you are, it's just fails and i end up wasting time. it's just easier/quicker to do it all at once. and then if there's any issues afterwards, you can deal with them individually. trust me on this...