I know what you mean by the joints -- I have no idea why mine aren't lining up, either! My plan is to use a small piece of flat rounded moulding on each seam once the whole thing's painted. I want to make sure that these things are still sectional, since my plan is to transport it to a nearby studio when we shoot. Not knowing how long it's going to take to build, I didn't want to build it onsite and have it be in his way for months on end.
My plan is to make all of the set sections in my garage, then truck them about 20 miles to the studio -- which has a lot taller ceiling and a lighting rig -- something that my garage sorely lacks!