what do you mean " rear pin that came with your big-sert kit"? The steel alignment dowels in the block don't come with the Big-sert kit. they were in your block, and hopefully they will go back in the holes. Did you mean to say the Big-sert, after installation is sticking up and preventing the alignment dowels from seating?

I am guessing the fiberglass dowel dropped straight down the return hole and remains upright...Can you fish tape on a wire to try and pull it back up (don't leave the tape down there)? Would a long, skinny, expanding claw grabber tool get it? I do think you should try everything to get it.