Guitar problem

[Tomes of Deceit]

The top couple strings on my guitar always go out of tune (even after I changed them), and certain frets just don't sound good at all, they buzz or make a dull twang instead of ringing clearly. I read that when you're changing strings, you shouldn't take them all off at once, but unfortunately I think I did that a few times before hearing that. I suspect I warped the neck. Does this sound like the issue? And more importantly, how do I fix it? If I remember correctly, I brought it into a guitar store once and the clerk looked down the neck and said he thought it looked fine and he didn't know what the issue was...