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I'm at a loss as to what is going on with my Mazda 3's 6 speed transmission. Below are a few details on my car and the issues:

Car: 2013 Mazda 3 i Grand Touring SkyActiv 6-speed Manual
Mileage: 67,500
Recent Work:
  • 62,000 miles - Drained factory transmission fluid around with the Ford Motorcraft XT-M5-QS
  • 63,500 miles - Bled the brakes and clutch master cylinder
  • 67,000 miles - Changed Motorcraft fluid to Redline MT-90 (75W-80)
Since buying the car at 9k miles, I've experienced intermittent unsmooth shifting into and Reverse and lockout in 1st gear, which is supposedly common. For whatever reason 5th and 6th gear weren't always as smooth as the others, but never gave me any issues. 1-2-3-4 were always buttery smooth and were solid up until replacing the factory fluid.
After changing out the original transmission oil, I started noticing a slight hold and notchy feeling into 2nd, crunchiness into 3rd, and the same with 4th and at some points experiencing a lock out into 4th where it didn't allow me to shift into 4th, but at no point did I experience a grinding.

I thought that it might be the transmission not liking the Ford Motorcraft fluid so I switched to Redline after hearing good things. After about 500 miles, I'm still getting the same issues, but what's frustrating is sometimes it shifts buttery smooth through all gears, but other times I get crunchy shifts. No grinds yet.

At this point I'm unsure if it's the transmission fluid (already spent $110 on fluid, and the OEM stuff is $29/bottle), the clutch master cylinder, or the synchro's in the transmission. Another user mentioned that it may be the pilot bearing. Any help would be appreciated, thanks!
 

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Get the relevant copy of the clutch pedal inspection test from the factory service manual (i.e. mm of distance of top of clutch pedal above floorboard when clutch starts to engage). The figure has to be above the specified-by-Mazda minimum dimension. This is described in detail... and tests for whether you are getting sufficient and full disengagement of the clutch when you shift gears. Start-of-engagement too close to the floor is bad... Insufficient disengagement is usually caused by air in the clutch hydraulics.

How to determine start-of-engagement? Detailed in the FSM... involves partially selecting reverse... and noting when the rattling occurs at the gear lever.

I note that you did bleed the clutch hydraulics... but still, do the test of pedal dimension... lest the bleeding operation was less than fully successful.
 
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