Since we're quickly jumping into summer heat, I'm interested in the effects of the cowl (Windstar) intake, which I think is early on your test list order. I've noticed my Jeep seems to pull timing pretty hard, at least that's my best guess as to what's happening, when ambient temps get above 90F. I'm interest to see what info you can pull from the dyno, intake temps and power figs, especially if you will do a few heat-soaked, hood shut runs stock vs cowl.
My anecdotal experience is it helped a LOT with allowing the engine to keep more advanced timing, even with the tune I previously had.
Here's the caveat though: it may be extremely difficult to get this to show on a dyno, unless the dyno is able to take very long full-power pulls.
In my experience, the gain largely occurs after having sat at full throttle for some time. In the normal setup, you have full power immediately, with maybe 10 seconds for the timing to start retarding, with it noticeably retarding after about 30 seconds to a minute in. The Windstar intake did not appreciably change the initial power level for me. However, it did allow that power level to be sustained indefinitely, and it is extremely noticeable when holding full throttle for 2-3 minutes.
The gain also seems to be largely independent of the engine RPMs as well. At 2,000 or at 5,000 RPM and full throttle, I would always get that sluggish feeling after a couple minutes. Now it does not happen much at all, except for very low RPMs (1500 or less), but it's seldom you'd want to hold full throttle at those low RPMs for more than a minute anyways.
Also of note, I suspect in my case power enrichment as programmed in the PCM does not really provide much of a gain if at all, and is instead there to prevent detonation. My tune keeps it out of PE except for when my pedal is absolutely to the floor, and I try to keep the pedal out of that condition (usually closer to 95% throttle) until pinging sets in. (Then the pedal is floored or I just downshift.)
Makes climbing the hills around here a lot faster for sure.