Clutch.
or clutch basket has grooves the plates are sticking in.
Possible warped or bent plate.
Possible missing washer/ spacer between the clutch pack and basket.
I'm thinking maybe it took more effort to move the leaver where it was but now its easier to move since you have more leverage or it feels more natural.
How does it behave without the engine running ?
Can you shift through all the gears without any feeling of binding ?
How does the shift lever move with and with out the cover on. Notice any binding with it on but not with it off ?
Here's something I would try.
With it idling and on the center stand, shift to first and release the clutch and then shift to second and on up and down with the clutch or without.
If its the clutch that is the problem, you will not notice anything while shifting up and down.
It would feel normal.
If its the shift mechanism, (forks, drum etc...) you will feel binding when trying to shift when there is no load on the back tire.
Hope this helps.

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