A couple of followup questions. Your point about the idle and WOT stops? What happens when they aren't properly adjusted? I'm not sure I understand the relationship to timing. Is there some black magic to setting these stops? Or just set it to factory specs?
As for the AFM installation, 45 degrees, got it. Are the physics of that as simple as 45 degrees? Or does it need to be adjusted depending on track conditions (banking, direction of the track (clockwise v. counterclockwise))?
The idle and WOT stops won't affect your dyno numbers.
The idle stop being right is more about:
1. Not tricking yourself, your mechanic, your dyno operator, your future owner, into making botched ignition timing adjustments.
2. Not fighting an 1000-1200 rpm idle when you are on track and trying to brake and shift.
3. Not asking the IAC valve to work too hard (i.e. same as #2).
A "tuned" AFM will tend to raise the idle speed - you want to adjust the idle stop to get it back down.
The WOT stop is more about not "overtwisting" the throttle shaft, which will then screw up the idle, and/or cause a throttle shaft failure. The throttle body flows plenty on the unrestricted 1.6 - you don't need it to be the last 1 degree open. So, when your helper has the pedal floored, you want to be out under the hood and find that the throttle plate has NOT hit its stop. As you stomp on the gas repeatedly, you want the hard "tapping" to be under your foot on the floorpan, NOT happening out at the throttle body. If the latter is happening, you are "twisting" the throttle shaft every time you floor it.
The TPS switch adjustment should NOT affect your dyno numbers. If it does, something is "weird" (either on accident or on purpose). Whether you have the TPS full counterclockwise, or full clockwise, it will still read idle at idle, and WOT at WOT. The purpose of the adjustment is to determine at what % the car goes open loop for street driving. It is a street fuel economy calibration.
Re: the 45 degrees: If you have it simply flat, you will see the A/F ratio swing around dramatically in LH versus RH turns. At 45 degrees, this is largely minimized - it is just a matter of how lateral forces are acting about the AFM door axis. So yes, banking will matter, peak "Gs" of corners when you are at WOT will matter. At vertical (connector down), the effect is almost eliminated, but now flow is fighting the AFM door "gravity", and the shape of the curve tends to change. Vertical tuning can work if you can shut your hood and retune "around" it.