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This issue I've had for about a year, and started when I switched out the regular shifter for a Barton short throw shifter to help me shift faster. The shifts at first were clunk (normal for a short throw shifter) and I got used to it (shifts became faster). After a few burnouts with the new shifter, the transmission would randomly refuse to go from 2nd to 3rd when I would shift quickly. Instead, I would hear grinding when trying to push it into 3rd. I turned to my clutch as being the issue, thinking that after 30,000 miles driving hard and doing lots of burnouts that the clutch was probably slipping, so I went ahead and switched it out for a hellcat clutch. The stock clutch was severely worn down when I took a look at it, so changing it out was a good idea. However, this didn't help the clunky shifts or the grinding from 2nd to 3rd. The grinding happens from 1st to 2nd as well, but its not as common as 2nd to 3rd.
 

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2020 Dodge Challenger Hellraisin Scat Pack
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That the behavior appeared after the aftermarket shifter was installed could be significant or just happenstance.

That the behavior has gotten worse and reading between the lines about how you use the vehicle the transmission could be getting "tired". Grinding can be due to worn synchros.

That not all gears are manifesting issues, only 1st to 2nd and 2nd to 3rd gear, really does suggests a hardware problem -- synchros -- not the shifter is at fault.

One possibility is the clutch hydraulic system is not operating correctly. If the system can't develop the necessary hydraulic pressure to ensure a fully disengaged clutch when the pedal is depressed or can't maintain the pressure, well, that's a problem.

With some cars the clutch hydraulic system shared fluid with the brake system. I found out the hard way the factory called for 2 year brake (and clutch) hydraulic system flush/bleed was quite justified to keep the clutch hydraulic system operating correctly.

You can try a test...

With the engine/drive train up to normal operating temperature and on level ground push the clutch in all the way and then move the shift lever from neutral to any gear, and then from whatever gear you selected to another gear. The lever should move ok and the transmission should not object with any grinding.

If after some time more gear selections become a problem this can be sign the clutch hydraulic system is not keeping the clutch fully disengaged. If just one or a few gear selections prove to be a problem this can be a sign of an internal transmission problem. Synchros most likely. Bent shifter linkage -- inside the case -- from forcing a shift or shifting too hard --- can also be a problem.
 
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