I don't want to be a wet blanket here, but IME with acrylic yarns, you can try blocking them and make them lay flat but when you wash and dry your squares they will go back to what they were originally. I've not used much wool yarn, only for socks, but I understand that wool blocks to size and shape; acrylic ends up doing what acrylic wants to do. If there is a significant size difference in the blocks you might try working a row of crochet around the smaller ones or do as salmonmac suggests and use a smaller needle or fewer stitches to match the size now that you're knitting looser. My opinion FWIW.
I'm glad you're hands aren't screaming at you!
This is the last time I'm frogging this project for the last time.