What type of clutch alignment tool did you use? If you used the generic type, they sometimes do not get the clutch lined up right. I use the ones with the splines that look just like the transmission input shaft. I have had some luck by putting the transmission in gear and have another person stick the driveshaft in the back of the transmission and slightly turn it to turn the input shaft while I wiggle the transmission and push it forward. Also put a light coat of grease on the end of the input shaft where it goes into the pilot bearing.