RE: ATA tolerance
I don't worry about ATA until it's at least 3/4" longer than it's supposed to be and don't usually do anything about it until it's a full inch. It's odd that your brace is longer than spec as well though. Usually it will be lower than spec when your ATA has gotten too long. But at only 1/4" on the length and 1/8" on brace height, you're in fine shape. Whatever other issues you've got, those are not the problem.