Ok. You're getting there.
If its a short as you suspect
By taking the connectors off (as you did the middle) you can narrow down the location. It sounds like you've checked to see if there was a reading between the connector and the alternator's output and there was none.
Do the same for the battery charge/supply wire.
Then check between one of the matching terminals on the bulkhead and ground.
-> If there is reading, then it must be inside.
-> If its open, check again with the ignition switch on 'RUN'. If its still open, then its one of the circuits that got disconnected when you removed the connectors.


The coil gets power from the ignition circuit.
During Start power from the starter switch goes directly to the coil.
When running power from the Run position of the switch goes through the resistor before going to the coil.

With points, the negative wire on the coil grounds and opens to build and collapse the charge. My guess is that an Ignitor I or II does the same. The positive is always hot (when the switch is in Run or Start).

Check the connections on the back of the ammeter.

Here is the wiring diagram for your car.
http://www.mymopar.com/downloads/1970/70_Dart_Challenger_Wiring_Full.pdf
If you look on Page 11 and 12 in the file (number 8-94 & 8-95 on the page header) You will notice that everything is tied into the Ammeter either directly or indirectly. Page 6 is the engine compartment (header #8-89) diagram.

First disconnect the pertronix ignition system and check for a short to be sure it isn't that.

Start by isolating where the short is. Battery side (probably not since it blows the fusible link), under dash, or alternator side of the engine compartment.

Note: There are 4 bulkhead connectors. 1 Large connector to one side of the bulkhead, 1 large in the middle of the bulkhead, and 2 small to the other side. I will refer to these in the following steps.


1. Close all doors, turn off all accessories, remove any underhood lights, Disconnect aftermarket radio's, and disconnect the battery. This prevents any erroneous readings from lights/devices being energized. Now connect an Ohmmeter to the large alternator terminal.

a. If it says there is a short disconnect the large bulkhead connector to the side. This separates the charging circuit from the under dash circuits. If the short goes away then it is probably under the dash but it could be a bad or chaffed wire under the hood. Moving the wires around will sometimes help you find it.
If it still says short disconnect the voltage regulator, ballast resistor and alternator checking for shorts after each. Still shorted? start unwrapping the wires to look for burns.

b. If goes away by disconnecting the large bulkhead connector to the side then start under the dash. Pull all the fuses and connect the ohmmeter to the back of the ammeter. Pulling the fuses prevents the erroneous reading from door open chimes lights etc. Disconnect both large bulkhead connectors. Does the ohmmeter read a short? If so disconnect the ignition switch wiring and the headlight switch connector. Both connect to the main harness without fuses. Still got a short? Double check the ammeter by disconnecting the wires and check each wire for a short separately without the ammeter connected at all. If the short goes away it is probably the ammeter insulators. The hands down most common problem in old mopars. That is why people are afraid to run them and switch them over the Voltage gauges. Check the ammeter terminals for short to ground.

c. Still got a short after disconnecting the ammeter? Then check the wires to the ammeter. If the red wire shows short then disconnect the middle large bulkhead connector to separate the battery side of the harness. Red is a straight shot the the bulkhead and fusible link if it's shorted you got problems in the harness. It will probably be on the black wire of the short is anywhere other than the ammeter or ignition switch because it feeds everything.

d. Black wire shows short? Disconnect every connector under the dash one at a time. Don't forget the wires to the AC/Heat. Still a short? probably a burnt wire in the harness. If the short goes away when you disconnect a particular device let us know which one.

Hope it helps

Power flows from higher voltage to lower voltage.
The Alternator supplies power around 14 Volts.
The Battery supplies power around 12.5 Volts when the alternator is not running.

When the alternator is running the battery floats closer to 14 and pretty much all the power is drawn from the alternator.

Wire R6 goes from the Alternator to the Bulkhead connector to the Main Splice.
Distribution occurs at the Main Splice.

Power distribution is hooked to the ammeter. It is wired to the ammeter from the Main Splice; the exact same way as the headlights, the fuse box and other circuits.

Thanks vey much guys, I'll have time Saturday to work on it. I will update then.

Update, my 47 year old alternator didn't want to play anymore. The short was in the alternator. Replaced the fusible link and put another alternator I had on.

Thanks again for the help.

Mike

Glad you found it. That's why I recommended disconnecting the lead at the alternator and checking each section separately. When it comes to trouble shooting electrical problems, divide and conquer usually is the best approach.

You guys help made it much easier. Thanks again.