Intersting points in the Blog.
In my professional capacity I'm an engineer dealing with large (up to & exceeding 747 dimensions & wts), very close-tolerance mating and moving structures, I would hope that, as mentioned in one of the previous replies, Boeing have addressed these issues. The one thing that concerns me is the removal of internal structures being necessary before the two sections would mate, under what is very definitely impled as being a force well in excess of what was originally calculated for correctly fitting parts.
This tells me that firstly, their tolerance analysis at the joints didn't tie in with the allowances that the separate plants were working to. Secondly, It looks very likely that their assembly jigs at the two plants don't mirror each other. Thirdly, it looks like they tried to fit the parts and ground to a halt before going back to the drawing board to ask how much force they could actually apply. I'd also query how the parts came to be finished off with the quoted 1 1/2 inch bulge on the left hand side of one of the sections within the mating area.
The other possibility that springs to mind is that the manufacturing plugs for the barrels have something unusual in their design and maufacture which means that the thermal movement in each plug is different from that of its complementary plug during the curing process.
Having done considerable work with composites for hot/wet & irradiated pressure envelope service for a previous employer, I'd have some concerns about the mating process used. It sounds like the end result is a joint which has residual stresses and strains in excess of the normal values. Whilst this likely remains significantly within acceptable limits, it does tend to show up a development programme that is in fire-fighting mode rather than setting the two parts aside until other sections with a more suitable tolerance build-up for each became available and coach-building finished airframes using these two "unusual" sections.
Oh Well, We all live in Intersting Times occasionally.
Best of luck in '08 to the guys in Seattle, I wish them well & hope they can get a full production spec hull in the air before the year is out.