Aha, that pretty much confirms the water pump is a goner.

As to your charging problem, either it ain't charging right or you're draining it overnight. With a DVM, check the voltage at the battery with a stopped engine (should be something like 12-12.25 volts). Now start the engine, with all major loads turned off (lights, wipers, fan, rear defog, seat heater), at a high idle (approx 2000 rpm) you should see something like 13.5-14.25 volts if you're actually charging. If not then the alternator brush/regulator pack would be a likely suspect followed by the internal diode pack.

If charging is okay then you've got a drain. One popular candidate is a sticking power window switch. In any event, you isolate it by pulling one fuse every night until you figure out which accessories are involved. Do your final diagnosis by disconnecting the suspect device and see if the problem goes away. Do not discount damaged wiring that is somehow shorting to ground without blowing a fuse. By 1989, the earlier rotten engine wiring harness problems were reputedly fixed, so count yourself lucky.