Thanks a lot!!
That's right, the puzzles were all handcrafted. The only automatic part of the process is a tool I made to compute the solutions, so I can just make/edit a puzzle and immediately check how many solutions it has. All puzzles have exactly one solution, except for two specific puzzles which were intentionally designed to have multiple solutions (puzzles 145 and 383).
All in all it took me about 6 weeks to make all puzzles. Making a puzzle can take anything from 10 minutes to 1 hour, depending on the size, number of holes, etc. On average, it takes about 25 minutes per puzzle. They were also tested multiple times (in different days) to verify that the difficulty conforms to my intentions and that the tricky spots remain tricky long after I forget the puzzle.