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Semi Update, I havent taken any time until today to really do some square 1 checks, but here it goes.
First I took it for a drive attempting more indepth tests. Pretty much same/same. Vibes in any gear (accel & decel) between 1500 & 2000 rpm. Ebrake 1 click and goes away, returns when released. Resting my foot at any amount on the clutch pedal while still engaged and I still got vibes until I reach the point where the clutch decouples and the revs drop to idle, then no vibes. Release clutch vibes return. While vibes are happening, if I tip in the throttle to match with road speed, vibes go away, but return if you roll out or add more throttle than coasting.

If I lift the car with a block under the trans, the whole chassis starts rising immediately, there is no sag or play in the Trans mount. About the only play I could create in the trans mount was 1/4-1/2" with a prybar between the 2 halves. The mount appears mint, unless Im missing something. I might have to completely remove the whole mount to check the bottom half of rubber, but I cant even force it to metal on metal contact with the prybar. The front and rear rubber pads on each side of the mount are free to wiggle about and not pinned between the 2 metal halves.
I loosened all 3 mounts, blocked the engine from the underside just to support it and gave it a shake then retorqued all the mounts to spec.
At this point I cant come up with anything pointing to the mounts being a failure unless the aftermarket PMM is not MS6 specific although it looks identical to the one I removed.

At this point I did a visual over the whole underside as I have done a couple times already, shook CV shafts, shook the exhaust, pushed and pulled on suspension, prop shaft, nothing loose, detached or missing. So I verified the fluid levels in the trans, pto and diff. Levels good. Pulled a sample of all three for inspection...all normal, no appreciable glitter and colour decent.
Trans has Ford XT-M5-QS with 40k and is due for a change...
20260916_150212.jpg
Pto and diff changed from Royal Purple to Amsoil SevereGear when rear axles installed...
20260916_151939.jpg 20260916_151954.jpg
I noticed the purple colour in the diff sample, perhaps I need to do another drain & fill. The royal purple had a friction modifier in it (dont know why I didnt catch that) and the Amsoil dosent. Not sure if a friction modifier would affect it. Oddly, the Royal purple was in the diff without issue for 40k. This all started after the VVT, Rr axles and fluid change.
At this point I am unsure where to look next or how to go about further testing to avoid a parts cannon barrage. I may attempt to run the car on blocks, but if done wrong that'll be sketch.
 
AI'd this...
Yes, the factory passenger-side motor mount (often called the passenger engine mount or upper right mount) differs between the standard first-generation 4-cylinder Mazda6 and the high-output turbocharged Mazdaspeed6. While the mounting locations and general subframe geometry in the engine bay are similar, the Mazdaspeed6 features a beefier factory casting and different stiffness characteristics to handle the heavier torque loads, vibrations, and movements generated by the DISI turbo engine and all-wheel-drive system
...apparently from AWR. I was suspicious because Mazda has 2 differing part numbers. The manufacturer of my OEM style aftermarket PMM lists it for MZ6 and MS6, but I know you cant always trust them...hell it does fit.
 
AI'd this...
Yes, the factory passenger-side motor mount (often called the passenger engine mount or upper right mount) differs between the standard first-generation 4-cylinder Mazda6 and the high-output turbocharged Mazdaspeed6. While the mounting locations and general subframe geometry in the engine bay are similar, the Mazdaspeed6 features a beefier factory casting and different stiffness characteristics to handle the heavier torque loads, vibrations, and movements generated by the DISI turbo engine and all-wheel-drive system
...apparently from AWR. I was suspicious because Mazda has 2 differing part numbers. The manufacturer of my OEM style aftermarket PMM lists it for MZ6 and MS6, but I know you cant always trust them...hell it does fit.
You'll be lucky to find an aftermarket manufacture that will get the different options correct. If their cheep version can fit multiple models that's how they list it.. Your problem sounds like a mount issue.
 
Ebrake 1 click and goes away, returns when released.
Havin deja vu from another recent MS6 thread, I'd inspect the two mounts on the rear differential. While in gear, the PTO is always spinning the driveshaft to the rear diff. There is an electronic torque coupler between the driveshaft and the rear differential that disengages at very low speed and/or when the handbrake is engaged.
 
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