For an example, as recently mentioned on another thread, my wife had thrown out a large scroll(?) box, and I had kind of agreed that it was not immediately salvageable. Over half of the wooden pins used instead of nails had broken, dropped out or otherwise perished, so the top, bottom and sides were pulling away, leading to general collapse. One of the metalwork ring fittings had gone from one side.
Given this box's condition, I felt no worries about using it for experimentation, so the pressure was off.
The main job was the pins/pegs. I removed one or two of the old ones to give me an idea of what we needed. As you can see in the photo below, there are many types of skewer or toothpick available in wood or bamboo. Bamboo skewer in Japanese is Take+kushi, = Takegushi 竹串. The kushi kanji is a perfect Shish Kebab. Sadly most of the bamboo skewers used in Japan are made in China, so it depends on how much of a purist you are. Search and ye shall find!
In some cases the old pin heads were stuck fast in the holes, so they needed drilling out, or redrilling alongside. There was a pattern to the pin placings, but I felt there were too few originally, so I halved the spaces and doubled the numbers. (About 80% of the pins were successful, but some failed for various reasons.)
I used a drill bit slightly smaller in diameter than the pin I was going to insert. Dipping the tips in hardware store wood glue 木工ボンド(Mokko Bond), forgive me this time, Henk-Jan, I hammered them in with a small hammer.
Later after they had dried, I sliced off any rough tops with a box-cutter (rough to the finger) and smoothed them off with a sander, actually a dirty nail-board/buffer. Now they have faded into the background and feel smooth to the touch.