I dont see any reason for lining anything up like you said. The only thing that needs to be lined up as far as I know are the splines the they slide onto the Trannies input shaft. Another little tip I learned from a mechanic today, is when you resurface/turn your flywheel, you can take sandpaper (something like this) and make an arched, back and fourth motion in the shape of a C, creating a rough surface going the opposite direction that your flywheel turns, so it grips better. I hope that made sense....
- Shane
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