I'm trying to find where the output wire from the alternator connects to the battery.  At the battery compartment there is only the main heavy wire.  Does the wire from the alternator connect at the starter motor, or ??

I don't think it connects directly to the battery, per se. The large red wire on the alt is connected to the ignition switch. horn relay, fuse box, and amp gauge, etc. The only direct connection is thru the amp gauge, which runs to the large terminal on the starter solenoid. 

Okay, that makes sense.  The amp gauge always shows charging, even after the battery has been on a charger.  When I installed the EFI and Vintage Air AC, they both recommended connecting the power directly to the battery (I connected them to the starter, which is about the same thing).  So this is after the amp gauge, so the current that the EFI & AC draw also comes through the amp gauge.  I'm not sure how this could be rectified. . .

One other confusing issue is after driving the car for a while, the battery should be fully charged, but if I connect my battery tender to it right after, it will charge the battery for almost a day.  The battery is brand new.

Once you shut the car down, the battery voltage will/should stabilize around 12.4v. Battery tenders/chargers always charge at higher voltage than that....otherwise they would just be keeping the voltage at 12.4. Once the tender/charger gets the battery up to 100%, it then backs off on the amperage to keep the batt fully charged(100%). You can have 12.5 volts on a battery and it NOT be at 100% charge, if that makes any sense. That's where the lower amperage charge comes in....it slowly charges up to the battery's full capacity, and then will cycle on/off to keep it at 100%, since batteries do self discharge when not in use. hth