Here's one of the puzzles that my dad put together while I was visiting. It's hard to see through the brown bottle, but the bolts, washers, and nuts are assembled inside the bottle as shown in the second pic.
The dowel is about 10" long 9/16" or 5/8" diameter. First hole is drilled about 1/2" from the end, the second is 1" further down. Holes edges are tapered slightly to keep the bolt threads from hanging when putting the puzzle together.