Too late now, but next time you try a flannel quilt starch the fabric after you prewash it. I wouldn't try less than 3" squares with flannel--it's way too supple for tiny details.
As for strip cutting & piecing, are you using a rotary cutter? Is the blade sharp? Be firm with it. You are the boss. You want to cut it, not carress it.
Can't sew a straight seam? Are you using a 1/4" piecing foot? If you don't have one or can't get one, try an old trick. Place a piece of masking tape (or some opaque tape) on the bed of he machine to the right of the needle, front to back. Be sure the left edge of the tape is 1/4" from the needle. Now when you line up the edges of yur fabric with the edge of the tape you will get a 1/4" seam. Just slow down and keep the edges of fabric right next to the tape.