Lining up the clutch pack is no big deal. People put way too much work into that.
Assemble the clutch pack, and BEFORE you put the spring(s) on to hold it tight do this...

The spacers hold a little tension on the pack. Put the pack into the basket on the bike and align all the plates while its loose. Then tighten up the bolts on the spacers to clamp it all together tight... then remove it from the basket and put the spring on.
It will slide back in the basket no problem.
http://jkozloski.com/pics2/clutch/Clutch%20101.htm