Stagpather,
That's a new one on me. It that unevenness uniform all around? If it is only on one side, the off-center chambering reamer explanation could explain it. If it is all around, I'll guess the grooves are not even in height across their width. You can test that by slugging with a pure lead ball or cast bullet and measuring it with a micrometer.
Shadow 9mm,
In your images it appears to me the throat angle may have been flattened some. There are cleanup marks in the middle of your grooves, but they are absent from the floor of the grooves as they approach the corners of the lands. This is common lapping with jacketed bullets as the lands indent the bullet surface but don't really cut it, so you get a radius on the jacket where it comes off the engraving mark. That part of it is not touching down in the groove to remove the tooling marks. Lapping with cast bullets leaves less of that untouched area. Look for higher pressure loads than you used with the Tubbs kit to fill the bore better and to possibly leave copper streaks where the groove cleanup stopped.
Not using coarse abrasive on a good barrel is common sense. If it was an air gauged button-rifled and stress-relieved blank like a Douglas, then you won't have constrictions to remove, so all you need is to polish enough that it can't grab copper anymore.
Constrictions can be a big issue, especially for shooting cast bullets. A button-rifled barrel that wasn't stress-relieved before contouring will be narrower where the contour is thickest, and you need some cutting action to bring it up to the diameter of the muzzle. The last military barrel I firelapped was in a Garand and was 0.0003" narrower near the chamber than at the muzzle, and to shoot cast bullets well, that constriction had to go. In the end, the cast bullets took 0.0005" off the throat diameter and about 0.0001" off the muzzle diameter.
Nick