Rather that if you have several spare parts, perhaps you also have more than one barrel remaining for your rifle. Of course I don't know that for sure. But I was trying to help, in case you were swapping barrels around.
Based on your initial post, and backing information you posted subsequently in your third post, "If I clicked right 4 clicks, I was hitting at 55 but splitting my 10 yard 3/8" target
..." you have confirmed through two matching scenarios, that your barrel may be aimed ever so slightly to the right, behaving the same in both scenarios (regardless of what the index marks say).
There is no guarantee that the barrel has not moved (or loosened) since you acquired it. So, my thought is that you might be better served by confirming that the receiver/tube screws are tight, barrel firmly secured, etc. Re-index if needed. I would think this prudent with any rifle -- including the mighty Thomas -- before any piddling with the scope. Because if the barrel/receiver -- as a base -- is not solid, any scope adjustments would be pointless.
If you've already done all this, then fine. Sorry for suggesting ideas other than playing with the scope/mounts as the first option.