A lot of the wonkiness will "quilt out". Part of the charm of old quilts is the wonkiness. I wouldn't cut down the blocks. I would hand piece them to sashing. You can use the sashing as your guide and ease in any excess block to the sashing. If a block is too short, I would hand piece in some neutral washed muslin as necessary. Honestly, much of the charm of these old quilt blocks is the wonkiness, which is a characteristic of folk quilts.
Because of the wonkiness, I would hand quilt. If at all possible, I would use wool batting because it is easy to quilt and is also true to the period of the blocks. My second choice would probably be Hobbs 80/20, which is also easy to quilt and, like wool, has some puffiness. At 80% cotton, it is close to the 100% cotton that would be true to the period. I would not use Warm and Natural because of its stiff drape, which would not be typical of the period (no needlepunching through scrim in the old days!). Plus, it is harder to hand quilt through scrim.