Before you re-install your transmission make sure you clean all the grease off the input shaft collar where the throw out bearing slides. Make sure that shaft is smooth. Apply a small amount of new grease to it so the bearing slides smoothly.
Also pull out the clutch fork, clean the pivot ball / fork and re-grease.
I also put a VERY light amount of grease on the transmission input splines so the clutch disc can slide freely on it also.
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1998 LX with a full HX swap + VX transaxle.
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