99 Accord - Not charging
 

Car died while driving... Tach and speedo started freakin' out, accessories started dying until the car died. New battery so I replaced the alternator. I'm still not confident that it's fully charging. My Door indicator lights are now lighting up when the E-brake is engaged. Now I'm getting engine codes for:

20 - ELD
61 - Secondary O2 heater
41 - Primary O2 Fail
25? - odd, doesn't exist.

Anyways. What could possibly be causing this. Short somewhere?

Yeah, you got a short somewhere

Would a short drain my battery while the car is running after an hour? I'm thinking the alternator isn't putting out power.

If you own a volt meter, check voltage when the car is running and then turn the car off.

Voltage when car is running: ~14.3 volts
Voltage when car is off: 12.2 volts

If you are measuring 14.3 volts when the car is running, then the alternator puts out enough power.

From what you are describing though, it does sounds like you have a short to ground (Chassis) somewhere.

check the connection b/w altenator and the battery and make sure that its all tight, not just hanging there.