cometic head gasket issue

I guess my question would be "How did the piston end up .045 out of the hole in the first place?"

Shouldn't the calcualtions have been done 1st and the correct pistons ordered for the application?

As far as the seeping goes, just run it a few times up to temp and it'll stop, if it doesn't then the block and or head finish is not smooth enough but I doubt that's the issue.