Clutch/Synchros?
 

I have a 2004 6Speed MT with 125k miles.
Shifting to 1st from neutral, 2nd, and 3rd gear has been hard for quite a time.(2nd gear being the worst) It also makes a thumping sound when I do. Gears do not grind, however very rarely it grinds when downshifting from 2nd to 1st.(Rarely as in 3 times in the last 3 months). It makes a thumping sound and isnt as smooth from a stop BUT with the pedal still pushed in and i shift back into 1st...It's smooth and there is no sound present.(If I let the clutch go and push it in again then shift into 1st/2nd;the thumping sound and the issue of hard shifting persists) 4th, 5th, 6th seems better but still isnt perfect. It seems like there is a force preventing me to shift Lol. I also have pulsation in my Clutch pedal. The only time I don't have clutch pulsation/vibration is when im putting it in neutral and sometimes shifting to high gears (5th/6th). Any insight on this issue is greatly appreciated.

when did you replaced the transmission oil?
hows the clutch pedal holding up?

Original clutch? If so it's prob ready for a clutch job.

Transmission fluid and rear Differential fluid was changed not more than 1k miles ago. Dealer said not to change the clutch it until the clutch starts slipping. I don't know the status on my pedal Lol.