...I get to analyze and diagnose this issue on converted fixie's on a regular basis at the co-op here.
The great majority of the bikes i see are either misaligned, because someone stuck the wrong OLD wheel
in the back or the front, or both. Wheel dish also comes up regularly as an issue.
The headtube faces is unlikely, but certainly if your headset is incorrectly installed, your handling will suffer.
You state your "dropouts are aligned", but say nothing about overall frame alignment (string test) to check the
rear triangles for equidistance from center plane, and don't really say how you checked fork alignment, including
how straight the front wheel sits in the fork.
Unless you are pretty good with frame alignment, I suggest you find someone who is, because you won't pick this up over the internet.
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