If you really wanted to be sure, you could reinstall the old eos switches. Not that i would recommend doing that, but it's an option.

I don't know enough to say for sure, but i imagine if the old eos were that bad they weren't passing much current. Now that you've got new switches in there, it's a much more conductive path leading to more juice making it's way through the flipper circuits (and pulling down some of the current from some of the other circuits)...just as zacaj said nearly all pins have a slight GI-dimming that happens when activating the flippers.

Only other things i could suggest would be to double check all your solder joints and wiring where you were working. Also, has the power supply board been rebuilt at any point?

Are the flippers substantially stronger with the new switches?