Ok, I think I see what you mean in the close up photo.
I would carefully trim the blocks to the same size, and just carry on. Be very careful when handling the fabric, the more handling the more distortion.
And once you've sewn the seam, leave it closed and pop it on the ironing board. Drop the iron on top of the seam and press down (no sideways movement at all, just PRESS). This sets the stitching in the fabric. Then gently open the seam to whichever side you are going to have it on, finger press it lightly open (do a small section at a time) and repeat the press thing with your iron to set it. Make sure there's no steam in your iron either.
You can make it work, take a deep breath and try not to stress. :-)