So, through my own stupidity (or inexperience) I spent a couple weeks last summer riding my first new bike without one of the spacers on the steerer tube. I now know you're not supposed to do this. I've beaten myself up enough about it, so go easy on me. For reference, it's an aluminum frame with carbon fork.

After learning that was the reason my headset was making weird clicks when I turned, I put the spacer back in and everything seemed fine. At some point after that, I don't remember when it started, I began to notice a creaking type sound coming from somewhere. I spent most of this summer taking various things off and lubing or greasing just about every possible millimeter I could think of to get it to stop. Finally, I had taken every part I am comfortable working on off with no success. I threw in the towel and took it to the shop. First he thought I had an excessive amount of flex in the forks, so I spent $350 on a new fork. That was not the problem. I just got off the phone with them and am being told that he believes I damaged the head tube(?) where the headset lives.
I do remember reading when diagnosing the missing spacer issue that too loose of a fork can stretch that just enough, like he is saying, to cause the noise. It doesn't affect the functionality. It's just one of those constant noises that drive you crazy.

So my questions are:
1. Has anyone dealt with this before?
2. Do I need a new frame.
3. If I do need a new frame, does anyone have a suggestion on where to get a decent price. I'm not opposed to BikesDirect and such.