Put something that you know is precision ground like drill rod or gauge pin in the collet. Make a witness mark on the pin, collet and holder. Check for run out and make a mark at the high spot.
Then loosen the collet and turn the stock 90 degrees. Re-tighten making sure the collet does not turn in the holder. Check run out again. Does the high spot move in relation to the collet or the holder? Make notes of how far out and what positions.
After you check it every 90 degrees, take it all apart and re-install it with all your original marks lined up to the same place. Check again. You should see the same run out that you first detected.
Next, go around again, this time rotating the collet in the holder but keeping the pin in the same place relative to the collet. Does the high spot stay with the mark on the collet or the holder?
This will show if the run out is in the internal bore or the external taper of the collet. It may be a combination of both.
Just as a sanity check, do the same test with a collet that shows no run out, just to confirm it is not the holder.
If the run out is in the bore, you may be able to true it up with a post grinder although that will change the size. Maybe you could make some metric collets out of them.
I'm not sure how to go about truing up the external taper but it could probably be done with a mandrel of some sort.
