This is just my view NorCalDuke. But the only reason I believe those bolt marks have moved is that your shock was part of the recall and was either replaced or removed to inspect. For piece of mind...I know this is a little tedious of what I am asking but you can always count the thread on the spring preload to a stock bike and if they are both the same I would say you are fine in the org setting department. Or you can check the length of the shock to see if that has changed.
Back to your tire wear. Now I have a few years of roadracing under my belt. 15+ years AMA and WERA and I have seen more tires than I care to see in that period. But there is NOTHING with the tire wear I see to remotely suggest you have an issue. With that said I can not account for how you feel on the track and what the bike is doing. But I do know that this bike is extremely sensitive to setup as far as going fast for expert/pro guys. But to the Novice/ Intro guy......for your tire looking like this you are good. Remember I am saying the tire looks good. I am not accounting for how you feel on the bike. ie unstable under braking, unstable mid turn, wobble on the gas mid turn, inconsistent feel in the same turn latter in your session. This is more about setup to get the bike handling the way you want.
I am going to go thur my phone right now to see if I have an example of my rear tire after 2 days of track time Expert/Pro sessions. You will see an example of a tire with great wear (as in good) that really does not look much different than yours with street and track wear. I hope this helps you feel a little more at ease.
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One other quick note. DO NOT let someone that is tuning zx10 gsxr R1 and CBR touch your bike unless they have a bunch of time working with 1199's or 1299's. I dont care how good they say they are. Its your arse on that bike. Protect it. With that said if you do have someone touch your bike. Write all your setting down and measure EVERTHING before they touch it. This include going thru your dash and taking a photo of your current settings.