After the whole thing is assembled and dried I applied red mahogany wood stain. This turns out to be a mistake in ordering.

The glue that soaks into the wood prevents the wood stain applying evenly. My advice is to apply wood stain to the wooden parts before fixing the box together in future. The 3mm Plywood is also quite good at soaking up the stain so a second coat after drying really gives it a great look.

I think a darker stain may be nicer on future boxes.