Obviously, the layout of a custom wood case will vary. But there are some specifics to watch out for when building it.
First, make sure that the motherboard is attached with spacers! This is both for reasons of heat and to ensure that there is no possibility of the motherboard being shorted out. Screwing the motherboard directly into the wood just isn't a good idea. Using rubber spacers is a good solution, but it may also be possible to use spare spacers that are laying around from previous PC builds.
If you're using components from a previous case, it is often possible to attach those pieces directly to the case without spacers, but do use your judgement. If the hard drive enclosure you've salvaged is merely a lump of metal with slots for hard drives, use a rubber spacer or something else to decrease vibration. If you're building your own custom hard drive case out of strips of wood, I recommend doing an out-of-case experiment first. Assemble the PC on your workbench, place the drives into their custom home, and turn it on to see if there are any issues with vibration.
Power supplies can be tricky. They normally attach to the rear of the case using four small screws. The wood you're using, however, will likely be too thick to use those screws. There are two ways around this. One is to spend time in a hardware store with a PSU in hand trying out screws until one is found that fits. The second option is to secure the PSU by building a wooden cage to put around it and then mounting the cage to the case. In any situation, be sure that the method being used to mount the PSU is secure if the PSU is at the top of the case. Dropping the PSU onto the motherboard is bad for your PC's health.