Congratulations on the purchase. As far as the knife, you seem like a discerning knife owner/buyer, to be able to find those issues on the knife with such ease. I would personally recommend that you send it to Spyderco for a refund, as its doubtful that they will be able to take care of it satisfactorily, since their business model is based on providing a good quality production knife, at a reasonable price.
I would then take that money and put it toward the price of a good custom knife. A custom maker in the appropriate price range (you will have to decide what that is based on the level of perfection you want) will then address all of your concerns personally, and you can end the cycle of frustration you are currently experiencing based on your expectation/price point situation. Of course, one little thing to remember, is that, as most makers will tell you, all knives have their flaws. Some are just harder to find. So, if you can't find a good custom maker, and it seems to be getting more difficult to find one who is able to offer absolute perfection in a knife while still trying to make a profit, whatever that is, you may want to make your own knife. Then you would have absolute control over how much satisfaction you can achieve, and surely attain perfection. Whichever path you choose, friend, I wish you all the best, and hope that you find what you're looking for.