Without a picture (and better yet, having your bike in front of me in person) I'm not convinced that your stem is misaligned. I know that everything above it can be misaligned (and realigned) due to the clearance feature I mentioned before...which is why I suggest you try that first. It doesn't require complete reassembly...just loosen those three bolts a little, realign the bar, retighten.
Carl Matson
Carl Matson