Just got it out again and realized that I actually had the top half of the whole thing already together, so I decided I needed to figure out how to just go on from here.
Got out my steam iron and attacked the joinings where it was puckered and got most of it to lie flat and the rest I've decided to just not worry about and hope it will sorta 'disappear' when I get to the quilting stage...probably going to tie at the troublesome intersections.
It's going to be six blocks by six blocks...have it at six blocks by three blocks now.
Hopefully the second half will go together better than the first! I've gotten a new machine since I did the other so it should be better.
Thanks for all the great ideas (and commiseration!).