Howdy
First off, holding a revolver freehand and shooting at a target 25 yards away is not a very good way to determine how accurate a pistol is. I know, everybody will say you should test it as you are going to shoot it, but that means you are including how well you can hold steady on the target in the test.
If you want to determine how accurate the gun is, without the human element, then remove the human. That is what a Ransom Rest is for. It clamps the gun in place, always recoils the exact same amount, and returns the gun to the same position for every shot. If you want to determine how accurate the gun is, forget holding it waving around at the end of your arm.
Without a Ransom Rest, the best you can do is shoot it from sandbags. Prop up some sandbags on a bench and sit down. Adjust the height of the chair and sandbags so that you can sight the revolver comfortably, do not crane your neck to see the sights. Whether you rest the butt of the gun on the bags or the frame or the barrel does not really matter. The point is consistency. Hold the gun exactly the same for each shot so that it recoils the same for each shot. Pull the trigger gently and consistently. Do all that, and you will find out how accurate the gun is, not how well you can hold on target. Remember, don't try to adjust your point of aim. You are not sighting the gun in, you are simply seeing where it prints shot after shot.
Regarding the throat size. You should not have to shove hard to get a bullet through the chamber throats. The correct sized bullet should slide through with minimum effort, you should be able to push it through with a pencil.
Here is the test I always tell folks to use. Remove the cylinder and point it at the ground. Drop a bullet into a chamber. It should hang up in the chamber throat. It should not fall right through. If it falls right through the bullet is too small for the chamber. If you have to shove it hard, it is too big. The correct sized bullet should just hang up in the chamber throat, and you should be able to push it through with a pencil.
I always suggest that for 45 Colt you perform this test with both .452 and .454 bullets, but you have already determined that .452 bullets are too big for your chamber throats.
45 Colt rifling has been standardized at .451 for a long, long time now, since about 1956. You could slug your barrel to make sure that the barrel grooves are .451 in diameter, but most revolver manufacturers these days are pretty good at keeping 45 Colt to .451. 44-40 is a different story.
The correct size bullet for any revolver works backwards from the barrel rifling groove dimension. Given that 45 Colt s usually .451, the correct lead bullet for that rifling will be .001 oversize, or .452. Then working backwards, the correct chamber throat for that .452 bullet will be just big enough that the bullet hangs up as I described. Somewhere between .452 and .453 will be ideal, allowing the bullet to slip through without allowing hot gasses to escape around the bullet. Hot gasses escaping around the bullet are a major cause of leading in the barrel because the hot gasses soften the sides of he bullet.
It sounds to me like your chamber throats are a bit tight. Measuring with a caliper is not a very accurate way to determine cylinder throat size, as you seem to realize. The tiny flats on the points of the caliper render readings of relatively small holes inaccurate. You could invest in some plug gauges to determine exactly what size your chambers are, and invest in a chamber reamer too.
Or you might want to give these guys a call.
http://www.cylindersmith.com/