Strange Engine bump / Cannot figure it out

[Partock]

2016 Mustang GT Premium Convertible. Feels good, feels like it runs good but has a strange engine bump that's random and is mostly present when cold. The engine will very briefly shudder when it makes the bump noise. No ping sounds, just a low thump kind of noise. Once I've driven it some and it's completely warmed up, it goes away. I haven't really captured it in a Datalog but the logs I have collected, I've sent to my tuner and they tell me everything looks fine. The car has 64,000 miles and in the last 18 Months I've done the following:
New Plugs (OEM)
New Coils (OEM)
New Injectors (OEM)
New MAF (OEM)
CAI (Air Raid)
Intake Manifold (IMRC Delete) (2018 Intake Manifold)
Tuned by PBD / 93 octane
New O2 Sensors (OEM)
New Vapor canister (OEM)
New Purge Valve. (OEM)

About the only thing I didn't' replace is the throttle body, but I did pull that off and clean it.
Power feels good, throttle response is good, just not sure I need to keep troubleshooting this.
Thanks

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