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Google what i said earlier. I believe it wa 03 and begining of 04 the transmission syncros go bad. If thats the case its gonna be expensive but a sure fix. Swap in an 05+ tranny that has the revised syncros. While your at it it would probably be a good time to upgrade cluth/flywheel. No sence in installing an old clutch.
yeah i have the same issue also an I figured it was the syncros, but yeah from all the looking around ive done, the 03-04 350z for the most part all have the same issue, the 05-06 350z has the revised tranny which ends with cd009. just keep in mind that if you get a new tranny that its for the DE not the HR because they are slightly different