Obviously my opinion is just that: an opinion, but here is my take on the matter:
A. The 1889 with the "gash" on the cheek was already scratched when you sent it in, but, in hand, the scratch was not as prominent as it appears in the pictures, and was missed by you.
B. The folks at PCGS saw something - cleaning perhaps - that caused them to think that the surfaces of the coin had been messed with. Maybe they erred on the side of caution; maybe not. Either way, it is possible that it will get the same designation if sent to any other service, including NGC.
C. The coin that ANACS graded MS64, and NGC graded MS65 was undergraded by a point by today's standards, and both services got the grade right.
D. The coin that was MS66+ and downgraded to MS64 was overgraded, again, by current standards, (and, possibly just overgraded period) and is now correctly graded.
E. No one at PCGS used a scalpel on any of your coins.
Hey, I know it stings to expect to increase the value of your coins, only to get what, to you, is an unfair slap in the face, but you can turn this into something positive, if you choose to do so.
If you will swallow your pride, and look at this experience as a learning opportunity, you can improve your grading skills, and save yourself some heartache, and possibly some money, in the future.
Again, just my opinion. Take it or leave it.