"What you have to do if you want to really get rid of those problems is change the MANUAL TRANSMISSION FLUID to a synthetic one. Wait until you get to around 4500 miles or when you are sure that the production of break-in wear metals is finished. Then, when you put in the new MTF mix in, it won't be further contaminated with any more break-in metals.
I STRONGLY suggest using REDLINE's product for our trannies. It makes the shifting BUTTER SMOOTH.
You should use a mixture of 60% MTL /40% ML-90 manual transmission fluid to have the right viscosity. I found out that this ratio is the best one for me.
That is pretty much the best stuff you're going to get for our tranny. It seems to provide the best shifts out of all other fluids I've tried."
manual-transmission-fluid-mtf-tutorial-t332828.html
I did this on the 04 Xterra with manual, and it shifts beautifully.