I am, your welcome.....
While I have never seen this exact issue in any of our panthers, I have had quite a bit of experience with electrical problems in cars that will at times see 100 amp loads at idle, couple that with idling for hours like that and high heat, and you get electrical problems.
I do know that Ford replaced battery harness's in 03/04 CV's due to a similar charging issue. The other thing I would comment on it the apparent use of the gauge in the dash for a measurement, I would recommend no less than a quality dvom, and preferably a calibrated unit at that.
While I don't think it's anything associated with the swap or the work, it is most likely just one of those things that happened at the most Inopportune time. I have seen new and rebuilt parts bad from the box, time after time, so without putting hands on it directly, one can only assume, based on experience or knowledge of the said circuit what the problem is. Fwiw, I have had bad cables, battery and alternator in the same car at the same time, so really, it could be anything.