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2024 Mustang Dark Horse — Whipple Stage 1, 10R80 — Persistent flutter/stutter + downshift clunk. Anyone seen this? (Taking it to Ford next week)

SC Dark Horse

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Dark Horse
The car: 2024 Dark Horse, Whipple Stage 1 (Ford-warrantied), 10R80 automatic, 11k miles, transmission/converter original and unmodified. Whipple's dual air intake system is part of the kit.

The symptom:
  • Flutter/stutter under load at constant RPM and speed — initially most noticeable around 1,980 RPM, but I've since confirmed it happens across all gears, not just that one spot.
  • Resolves instantly the moment I touch the throttle, either direction (on or off gas).
  • Gets worse when the transmission is fully warmed up — not cold, which seems to be the opposite of what a lot of 10-speed shudder complaints describe.
  • Progressively gotten worse over time.
  • New: a clunk on downshifts, and both the flutter and clunk feel like they're coming from the middle of the car, right in front of the dashboard — roughly where the transmission/front driveshaft area sits.
Timeline / what's been ruled out:
  • Flutter was present before I had the rear end replaced (unrelated repair). The rear end swap did produce a new squeak, but the flutter itself predates that work entirely, so it's not caused by that.
  • Driveshaft/pinion angle was measured by a shop after the rear end replacement — came back within spec, so I've ruled that out as the cause of the flutter.
  • Flutter has been present on both the stock Ford tune AND the Whipple Stage 1 tune. Whipple confirmed directly (twice, by phone) that their Stage 1 tune is engine-only — it never touches transmission/TCC shift or lockup calibration. So the transmission calibration has been the stock Ford cal this entire time, across every configuration.
Diagnostics done so far:
  • Whipple reviewed the engine/supercharger datalogs twice (two different calibrators) — found nothing abnormal, called the most recent log clean.
  • A local speed shop's story shifted a few times. First said AFR was "insanely rich," then said trans looked clean with no TCC oscillation in their data, then landed on recommending a full engine+trans custom tune. I never got to see the underlying data for any of these claims, so I've held off on that route for now.
  • I pulled a longer datalog myself and had it analyzed in detail. Findings: the "rich" AFR readings were all tied to normal DFCO recovery enrichment after coasting — transient, not sustained, doesn't support the "insanely rich" claim. But there IS a real, repeatable pattern of sustained knock retard (spark pulled up to ~5°) recurring in top gears (9th/10th) right around 1,600–2,000 RPM under boost, and the magnitude increased as coolant temp climbed over the course of the drive — which lines up with my "worse when warm" observation. Sent this to Whipple, who reviewed it and said it looked clean/fine.
  • No TCC-specific PID data (slip speed, duty cycle) has been captured yet by anyone — that remains the one piece nobody's actually pulled and shown me.
Current hypotheses I'm weighing:
  1. Torque converter — clutch material/lockup behavior struggling to hold clean partial lockup under the added torque from the blower, possibly compounded by heat as fluid thins when warm. Would fit the all-gears symptom and the warm-vs-cold pattern.
  2. TCC calibration hunting — stock Ford lockup/PID tables potentially not well suited to the modified torque curve, even though the tune itself came from Ford.
  3. Something mechanical at the trans/front driveshaft — mount, U-joint, or slip yoke play, given the downshift clunk and the localized feel right in front of the dashboard.
  4. Engine-side knock retard may be a contributing factor but probably isn't the whole story given the symptom is present in every gear.

Taking it to Ford next week for a proper transmission diagnostic (still under warranty) — trying to gather as much real-world input as possible beforehand so I can point their techs in the right direction.

Questions for the forum:

  1. Anyone had a similar flutter/shudder at cruise on a Whipple Stage 1 / 10R80 combo, especially one that's worse warm than cold?
  2. Anyone dealt with a downshift clunk localized to the trans/front driveshaft area which turned out to be mount, U-joint, slip yoke, or something inside the trans itself?
Thanks in advance!
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