Um, if your clutch disk doesn't hold the input shaft tight enough to keep it from wobbling when the clutch is out, you officially have the worlds crappiest clutch disk. The disk won't move AT ALL then the clutch is disengaged, so the only slop would be from the splines on the input shaft. And that should be just about negligible.
Now, if it were mis-aligned that would be a problem all the time. I would still bet money that it would sound different with the clutch engaged vs disengaged though, because the input shaft would not be spinning in the pilot bearing with the clutch disengaged.
But in the OP's case, he just changed his clutch, not his bell housing, if I'm reading his description right. If that's the case, alignment shouldn't be an issue unless he also removed the bell housing.
