Glad to hear that you got it worked out. I have run into the same issue w/ Model1 Sales. In one case, I had to throat and finish ream the chamber in order to get a round to seat fully. For future reference, the green scotch pad method is the least invasive way to clean up a chamber. I takes very little away in terms of actual metal. If you followed the tecchnique you described, you should be fine! I use an in and out technique to create a swirl pattern inside the chamber, kind of like polishing brake slave cylinders or V8 cylinders.
One thing to always remember: Never mess with the gas port size! A burr in the bore can ruin your whole day! Not to mention the really heavy recoil if you overbore it! Accuracy tends to suffer a lot under these circumstances.