After mulling around what I was going to do with this bike for three days, I was convinced to just put it back together and use it. It's served me well in the 6 years of owning it, never having tracking issues or anything resembling having a bent frame.
So... I wound up putting in new steering head bearings and races, rebuilt the forks, and needed to send my front wheel out for new bearings and shims (I bent two pin wrenches trying to get the hub nuts off). It's all back together and working wonderfully. As expected, the steering and cornering is a bit better since the rebuild, and there are still definitely no signs of a bent frame. I tested the bike at speeds from 0-110mph and it tracks straight and stable. Took my hands off the bars doing 60mph, still straight and stable, whacked the bars to intentionally destabilize the front end, and corrected the wobble by gently grabbing the bars - in other words, there is nothing wrong with this frame.
The tweak is still there, but I immediately forget about it once I'm on the road.
I remember watching a Jesse James special many years ago, I forget what he was trying to make, but he said something along the lines of "when you're bikes not feeling well, you're not feeling well." It's simple, but it's so true, and I think it's difficult to convey these feelings to someone who hasn't built a bike or a car. Having this bike OOS drove me nuts, I couldn't sleep right, everyday I thought about the problem and was dying to fix it. Everyday I had to wait for a part or tool to come in (btw, the CycleWorks bearing puller/press made life really easy), was like anxiously awaiting Christmas as a kid. I stayed up till 0010 last night putting everything back together. Even though I got up at 0445 that morning, I got in the zone, and then immediately test rode it. Knowing that everything was together, fixed, and didn't need any adjustment, I went upstairs, washed, kissed my wife, and slept like a baby.
Everything in my world is back in sync