SOURCE: I have an 04 yz 125 that won't shift into 2nd but
2nd gear is at the bottom of the shafts if the tranny is stacked in the mag side case. So it is controlled by the bottom fork. You should be able to shift it thru all the gears by turning the shift drum. Make sure as you shift the shafts stay all the way in the output shaft and idler shaft bearings. As you shift it, look for full mesh between the wheels(shaft that goes to the clutch) and the gears across on the output shaft.
If that all looks good, the shifter cluster(on the end of the shift drum, with the 2 dogs that engage the notched wheel on the end of the drum) may not be lined up properly. If the gears and shift drum are new, I'm thinking I'd look there first. Good luck!
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