How do you make the handlebar stem straight?
A problem many hit when trying to straighten the stem is that they end up aligning the stem with the bike while the wheel is almost straight. A degree or two isn't noticeable until you are riding and then it really bothers you.

Instead of trying to align three things (bike, stem, wheel), turn the wheel about 45 degrees. Now align the stem (I generally do it with the wheel trapped between my legs and the bike in front of me) to the wheel. It's much easier to ignore the bike when it's not even close to in-line.

Happy riding.