So AFTER the engine swap it HAD been working?
An aside, do ya have a shop manual? Since you have a 66, you are in luck, and can dowload one over here:
http://www.mymopar.com/index.php?pid=31
Der linky
http://www.mymopar.com/downloads/servicemanuals/1966_Plymouth_Service_Manual.zip
You'll have to play with page numbers, because they appear in your viewer 1-8xx, rather than (electrical section 8-1, 8-xx, etc)
This could be as simple as worn brushes, or sticky brushes that are not contacting the rotor slip rings.
First, are you using the newer 72 alternator? If so, it has two field connections (the smaller spade "push on" connectors) and if you are using your older 69/ earlier regulator, you needed to ground one of the push on field connections and hook your original green field wire to the remaining one.
A QUICK CHECK
Take your meter or even your test lamp and see if you have power at the big output stud on the alternator --the stud with the large black wire
Next, take a clip lead, remove the green field wire, and clip the lead from the stud to the field connection on the alternator
Start the engine, gently bring up RPM, and see what the ammeter does. It should charge if the alternator is OK.
IF not time for more checks
With the clip lead still connected, clip your multimeter from ground to the big alternator output stud, and bring up engine RPM. The voltage should go above 12.5, and the higher the engine RPM, the voltage should go up. If it goes up higher, say, 15V (Don't allow it to go above about 15-16) double check the ammeter. If it shows no charge, there is a bad connection in the charging wire For an additional check, put your meter across the battery and see if the battery voltage starts to go up with RPM
If the above happens, you probably have a bad regulator, or problems in the regulator wiring.
To check this out, hook the green back up to the field at the alternator, "as normal." Unhook the two wires from the regulator and clip them together. Start the engine and again see if it charges. If so, replace the regulator
Buy a good one. If you are using the 69/ earlier system, buy either a Standard brand VR-128 or a NAPA / Echlin VR1001 Yes, these are expensive. Yes they work.
NOW if none of the above seems to get you anywhere, read this MAD article about the pitfalls of Mopar bulkhead connectors. Study the diagram down the page, which shows how the main battery feed and main charging wires come into and out of the interior through the bulkhead. These two are very prone to damage and failure, BUT THERE are others, such as the "ignition run" circuit, and the headlights hi/ low beam
In fairly rare cases, connections at the ammeter can be bad, or the molded factory wire ends fail internally. More rare is failure in the ammeter itself. And even MORE rare is what is shown in the diagram as the "welded splice." This is a factory welded splice in the black ammeter lead. I doubt it is associated with this problem
http://www.madelectrical.com/electricaltech/amp-gauges.shtml
