After driving to work and back, I find that all the guages read less than before, except the voltage which has always sat just on the positive side of center, however when I installed the new IVR, it did regester a higher charge rate for a few seconds, then dropped back to center+.

The new IVR is not motorcraft, it's Standard... I have a used IVR I picked up from the U-Pull-it. I'll try one to see if it is any different later today. While I'm in there I'll take a look at the "Y" brace connection.