charging issues on genIII swap

You are running a pre 70 regulator?

Most these voltage problems are caused by grounding / voltage drop problems

Sometimes it can be a defective regulator. Especially suspect are the older ones "relay" type. Look under the base of yours. If there are two large wirewound resistors, it's a relay. Most older type (pre 70) regulators have "by now" been replaced, and most replacements are actually solid state inside the "old type" box

Learn about voltage drop. It's much easier to measure drop with your meter directly because you don't have to take two readings and subtract.

EG: Hook one probe of your meter to the VR IGN terminal. Hook the other probe DIRECTLY to the battery post, IE stab the probe right into the top of the post. Obviously if you have a trunk--mount battery, you'll need a long wire extension. A piece of no14 or so is just fine.

With the key in "run" but engine stopped, set the meter on low DC volts. You are hoping here for a very very low reading, the lower the better. More than about .3V (three tenths of one volt) means you have a voltage drop problem

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Check the ground side. This you do a bit different. Clip one probe to your meter direct to the battery NEG post. Stab the remaining probe into the mounting flange of the VR. Stab through any chrome, paint, rust. This time, you want the engine running, the battery charged up after starting.

Take the reading with the engine running at a good "fast idle" or "low cruise" and first with all accessories off, and again with heavy "stuff" like lights and heater turned on

As before, you are hoping for a low reading, lower the better, and zero would be perfect. More than .2--.3V means you have a problem

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If these tests show OK I would try a different regulator. Buy the best one you can find. One that used to be considered "great" was the Standard / Blue Streak VR-128. The NAPA / Echlin equivalent is VR-1001

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Also just for grins, check your running / charging voltage. Check this right at the battery, and then up front wherever your power is pulled off to feed the car

Tell us a bit more about power distribution in the car. I detest having to use a crowbar to get information out of people. I'm guessing you have a trunk mount battery.
thank you.. battery is up front..