Water leaks, electrical gremlins 1987 300TD

Hi all, my mother's car, a 1987 300TD with 180K miles has some issues - water leaking into the cabin and electrical shorts. This all started a few weeks ago when we got several inches of rain in a short period. I'm told that water was dripping out of the ignition switch!! I found that the spare tire area in the back was 4 inches deep in water. The drain was plugged.

The battery was a MB 100 amp battery which is about 12 mo. old. Ignition seemed to work, glow plug cycle went through fine. Then just a "click" which came from starter solenoid. Charge on the battery was 12.4v. I switched the MB battery with the battery from my 300E and the car started fine. My battery had about 12.7 or 12.8v. The car started for about 3 days but now is back to "click" on ignition and no start.

I cleaned the battery terminals and I cleaned the battery ground connection.

The starter is a rebuilt Bosch unit which I removed and had tested. It's fine. I'm hoping to get some tips on where to start diagnosing. Tomorrow, I plan on testing the fused circuits to see which, if any, is drawing current. I suppose the alternator could be bad?? How can I test the alternator?

Thanks in advance for any tips/tricks. I'm an avid reader of this site, about every day.