Hey twin still uckfaying chapped you took that username,
Explain this in great detail (or better yet draw a picture) of how you are measuring your clearances. Once I see how your calculating it, I'll comment on your method. Torquing the heads won't effect bearing clearances, you do that for piston to dec or degreeing, ect. Since I'm assuming this is a subi engine, make sure the block is torqued to spec when checking your clearances.
Just from first glance your factory specs seem really tight. 0.0004 is ridiculous.... so I'd double check the spec on that. Are you sure its not 0.004?
Do you have plasti gauge? It's your friend if you want to double check your measurements.