You are correct the negative toe will cause (slight) straight line wondering and slight oscillations during cornering. The extreme conditions you describe may be enhanced due to type type as tires can have a profound effect on performance.
As far as body design and wind induced anomalies, I can't take credit for that one as information provided related to how a vehicle performs during windy conditions or at speed. I had an opportunity to talk with a retired NASA scientist by the name Albert Muller this spring. He studied my designed and viewed and pointed out the possible flaws.
From a strictly aerodynamic view a traditional trike has an advantage as the center of force is behind the center of mass so like a dart with a tail it will naturally fly straight. Put the front wheels ahead of the center of mass then add a large cowl and according to Mr Muller the dart becomes unstable. Pretty easy to visualize.
Of course my reaction was "But Albert I don't drive 8000 mph" he said "good point".
He than asked me "when you drive in the rain, where does the water go?" He said this is the poor mans wind tunnel, you watch where the water spray off the tires ends up and that will tell you just where your weaknesses lie.
In any case 2-1 configurations with a narrow and rounded nose cowling will do well at normal to high speeds and those with larger frontal areas will perform less proficiently.
I now incorporate wind testing in all designs.
Getting back to the spyder. The width to length wheel ratios are spot on along with the fact the spyder places most of the mass as close to the front wheels as practical. These factor dictate a good stable straight-line path along with low lean predictable cornering. I think Bombardier did a great job in the design and layout however may have an issue with tire choice.
Toe will have as stated a slight affect on stability and yes negative toe should be avoided. Unfortunately none of the other critical steering adjustments are readily adjustable so it's just toe and tire choice.
The aerodynamic wander normally rears it's head at 40mph plus and is very much like the feeling you get when riding across a steel slated bridge deck. It's not extreme or dangerous but somewhat consistent. This wondering or oscillating does not amplify with speed and at points may actually diminish. More caster and positive toe along with better tires will all aid in reduction of this effect.
It is also one of those things most riders will become used to and in time not even notice it's there.
I must disagree with some of your definitions and and applied concepts. If the toe is incorrect, towards a toe out direction, the word slight in regards to wandering when traveling straight must be based on the severity of toe error, and the comfort level of the driver and passenger. Your experience of 100k miles, and I assume this was on machines with oem alignments, may have been slight for you, but others may find it extremely unnerving.
The degree of toe out error will make the machine less stable with more toe out and more stable as the wheels are made closer to a proper toe setting. In simple terms it is a balance of forces, and toe out is an unbalanced setting. Using the example of how a tail heavy dart wanders in the longitudinal axis, and your explanation of riding over a grated bridge are fine examples of toe out. Toe out does not allow a hands off the bars while traveling straight ride. Proper toe in will. Also, proper toe in will induce a natural self centering of the wheels and allow the machine to naturally flow out of corners as the wheels have a force on them returning them to straight. Toe out does not accomplish this. Toe out, causes the machine to have a tucking effect to the inside of the corner and relies on centrifugal forces alone to exit the corner. If the machine was utilized on a race course with a an experienced race driver, he would prefer slight toe out to allow better turn in. However that situation is a very focused environment.
Your friend, Albert Muller, has some interesting remarks. In regards to rain, on aerodynamic surfaces it is a great tool I have used before. The best use is for flight vehicles where laminar flow is needed. Similar to tufting with yarn, but provides better entertainment and a more accurate result of an entire chordline or surface of a panel. Watching rain spray off BOTH tires to prove something would be difficult if not impossible. We have ridden in the rain. From my experience, I can only watch one tire at a time, and not for long. Not sure where his comments were headed, uness he was considering a sophisticated camera and data acquisition setup.
If you mistakenly substituted watching tire spray for watching airflow across a body panel, that is easily more doable on the frunks upper surface and fenders.
I do enjoy the concept of using the dart example in regards to stability. One consideration I have when reading those remarks is that there is a transition of force in a dart or arrow that a Spyder does not enter into. A dart when launched is held forward, so the input force is towards the front and the mass is forward. The mass remains forward with an aerodynamic cross section that is symmetric. The aft body of a dart has stabilizing fins, so basically the entire engineering is based towards stability.
With an arrow launched from a bow, or even a rocket with aft propulsion, these too have a center of gravity like every object. There is an optimum CG, which could be adjusted via a weight tip at the nose and tail feathers aft. In simple concepts, the arrows body is a constant weight at each station section along the entire body length. Being propelled from the rear, like a Spyder, this induces a force that must be stabilized. For a flight vehicle, air is the supporting media, so fins on the aft body control this.
A Spyder is an aft propulsion vehicle also. The media is different being grip to the road and the effect of the three tires all come into play. Assuming the rear tire is properly aligned and the chassis is built correctly, the line of thrust should be centered between the two front tires. Stability for the rolling chassis must come from the front tires. As you mentioned, tire replacement could be a solution, however for those with newer machines sporting the 15" wheels these choices are limited. Those with 14" wheels may find a better choice. Regards though, tires will not correct toe misalignment, simply mask it and the tires will still scrub, resulting in lower top speeds and reduce fuel economy.
Turning the page to center of of aerodynamic pressures. Your ideas of better aerodynamics is solid for any vehicle. Reading your words it almost sounds as if you are designing a new vehicle or planning to build body panels for an existing vehicle. With the Spyder, all aerodynamic and CG calculations must include the vehicle itself AND the rider or riders. Line of thrust is basically moot since it runs straight down the vehicle. unless you plan to accomplish crosswind buffeting effects. Unlike an aircraft, space vehicle or enclosed land vehicle, the riders on a Spyder are a huge part of the equation for aerodynamics. Additionally, the riders themselves, having mass or weight, will counter the instability you mentioned of the front end aerodynamics. Also, like an arrow, launched from a bow, having rear thrust, the riders act almost similar to a stabilizing fin as air passes around them. If one recall the recent commercial of a sport bike in a wind tunnel, and the engineer comes out to the rider and mentions all this paperwork must be completed, it was obvious none of the paperwork, as it blew from the engineers hands went onto the rider. Even with a two wheeled sportbike, the rider is positioned for low drag and aerodynamic stability.
When accomplishing calculations or testing on a Spyder, please consider that entire front end is not opaque to airflow. A very large percentage of the direct drag from the profile does not exist but is rather air passing towards radiators and classified as cooling drag. Cooling drag, while important is not always blunt and does change the numbers in calculations.
Our sidebar discussion, based on your comments regarding forces and aerodynamics has steered this topic well away from alignments.
I will not dispute your 100k of experience. I do hope you were involved in testing for optimum toe settings away from a computer and perceived formulas. Road experience with back to back testing of various toe settings proved to me the small change in adjustment was a large change in control.
In regards to you aerodynamically testing all your work, all the best with it. There have been many an aerodynamics engineer slap their forehead once the guys with practical experience get a chance to sort the entire package.
Again all the best with it.
PK
Riding time, riding time the light will go on. 
Now I've got just under 30,000 miles on my spyder and I'd never go back to 2 wheels. This thing is just TOO MUCH FUN!
