If I had to pick one thing it would be the difference in head gaskets.
If the difference in head gasket thickness were enough- and that could be a relatively small amount we're talking about here- that alone could account for the shims returning the lifter preload to a more normal position.
If the lifter retainer clips were missing, the shims wouldn't have fixed the problem so I think you can eliminate that as a possibility.
If different pushrods were used, that could have caused it, too. But it sounds like it went back together w/basically the same parts it started with.