One of your problems may stem back to the BLO. Polymerization (hardening) of BLO is a very slow process. It takes weeks, months, even longer and may be contributing factors to the problems with layering. However, having said that, it just may be that you did not allow enough time in between coats for drying and insufficient block sanding in between coats. From the pictures I really can not see the problem well. I would let it sit and cure/dry before doing anything.