what are you having trouble lining up? The transaxle input shaft splines with the clutch disk?

If you are unsure of the clutch, take the PP off, and fit the clutch disk onto the transaxle's input shaft with the clutch not yet installed. if it fits, then the clutch disk was not lined up with the pilot hole in the flywheel. Once that's lined up it can sometimes be a pain lining up the transaxle. I recommend 2 friends for that. 2 people to position the transaxle, and one to push it in place. (you have to control 6 degrees of freedom, so 3 pairs of hands makes it immensely easier to put it in place).