From what you are describing, it sounds as though you are checking the bellhousing parallel to the block? Have you verified the register bore? That is the measurement that is critical as well.
This is an article from Lakewood, and will be the same for any bellhousing.
The .004 could be paint on the block, bolts not torqued the same as well. More information is required.
http://www.gt40s.com/forum/attachmen...1&d=1292251774
Sean