The pocket is fine don't worry about that. Mine is a tiny bit off too, but as long as the stitching matches well, all is good. The CC though I am EXTREMELY picky on and do my very best to find ones that are not lopsided and are in the middle of the diamond as best as possible. However, guess what?
Your CC is not off by very much and you can actually turn the CC a little bit and it won't damage the bag. I figured this out the other day and was soooo happy! My new black caviar WOC I would say out of 1-10, had a 9 in terms of the CC on the front being straight and not crooked. I however wanted it to be a 10 so I took my finger nails and ever so very slightly lifted one side up and one side down and I couldn't believe what I saw! It moved a tiny tiny bit, enough where it is now perfect. The leather is totally fine, no harm done. I don't think it will work if it's seriously lopsided, but if the CC is almost perfect, it works like a charm!!! Probably only works well on caviar though like ours, as I can't imagine it would on lamb, but maybe. Give it a try on your bag and see if it will fix it enough to where you feel more at ease
In regard to the flap, I've noticed all are a little wonky but if you move one side up or down it should even itself out. Unless you took a ruler and found the measurements were actually off?