You might want to try "true-ing" blocks to size and shape before sewing them together. Sharon Schamber has videos on
http://www.youtube.com that demonstrate how to either shrink or stretch a block to size. If you do that, your blocks will no longer be wonky and your top will lie flat of its own accord.
It does sound as if you are stretching the blocks out of shape when you iron. Also, unless a pattern is very complicated (involving arcs or circles), it's usually unnecessary to pin a lot to achieve sewing accuracy. It sounds as if you may be stretching your blocks out of shape when you iron.