I don't have any advice but I have learned, on this forum, that flannels shrink like crazy after getting washed so it's a good idea to wash the fabric before cutting it.
One thing that I have done is the past when using fabrics that don't play by the rules is to pin, pin, pin and pin some more. I ease the longer fabric onto the smaller fabric by pinning at both ends, then at the center and then evenly along the length of the seam. I hope this makes sense to you.