2 things to check: looking at the schematic there appears to be a 3-amp slow-blow fuse under the playfield for each flipper. The one you want to check will have a blue/yellow wire on one side and a red-yellow wire on the other. Pull the fuse out and test it for continuity with your meter.

It's also possibe that the female connector for the flippers at the CPU (CN6) could have gotten damaged by the battery leakage if it was that extensive. It couldn't hurt to re-pin that connector. (Though I think you may have ruled that out with test 3)