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Wow, two great questions! To answer the first one regarding the barrel liner o-rings...I always remove the o-rings because there is really no good way of securing them so they are in the same place each time. Accuracy can be defined by one word: Consistency. So either leave them off or support the liner a different way that will remain consistent. One way of supporting the liner inside the barrel tube is to wrap tape around the liner in several spots until it just fits snugly into the barrel tube. This way it is supported the same way each time you take it out and put it back in. You might want to test your own rifle by shooting some groups without anything on the liner, and then with supports of some kind on your liner to see if there is any difference in your rifle's accuracy.
As to the second question: When you over tighten the grub screw on the rear block that holds your barrel tube in place, it pinches the barrel liner inside and makes it hard or even impossible to rotate or remove the barrel liner. So when you are going to rotate the liner to each of the new positions to shoot test groups it is important to loosen that grub screw first. Then of course you must remember to tighten it after you rotate the barrel liner to each new position. It seems that most people tend to over tighten screws and especially that grub screw. I have had dozens of guys over the last few years contact me to ask why they can't remove or rotate their barrel liner to index it, and it is always because that grub screw has been over tightened with an Allen wrench. Maybe this is why the original Impacts had a thumbscrew rather than an Allen screw?
One last thought to share...Once you get your liner indexed to the sweet spot that gives you the best accuracy, you can make a permanent registration mark so that you can remove it for cleaning and reinstall it to the exact same place each time. And each time you reinstall your liner it will shoot exactly the same way each time.
...To answer the first one regarding the barrel liner o-rings......So either leave them off or support the liner a different way that will remain consistent.