I don't think headspace is the issue. You seem to have done that correctly, and it should not be installed any differently.
Are you saying the bullets must be seated into the case deeper than before so as to not touch the rifling? If so, the chamber was not cut as deep as before. (The rifling starts sooner?). The only fix for that would be to have it reamed deeper. Not sure it is worth doing if you are getting good accuracy. I could be wrong, of course. :)
I imagine you are getting more speed from the factory loads b/c of the longer barrel. That would make sense to me.
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