On our trip we crated our bikes 3 (yes, three!!) times. What we discovered is, that wherever you want to ship your bike from, there will be someone who can build the crate for/ with you.
In Indonesia we got beautifully hand-crafted boxes made from some kind of mahagony wood, really too bad we had to leave the things behind in Singapore. I think it's going to be a lot easier if you use the help of the shipping company to build the crate. They'll have the right people, tools and materials. And if you'r not shipping out of Japan or western Europe it won't cost you an arm and a leg.
We left both wheels on the bikes and strapped them down to the (rigid!!) base grid. But you'll save some volume (=money) if you take the front wheel off, even much more if you take the bike apart even more. In Mongolia we met some Guys who had flown their BMs from Austria. They had taken both wheels and the fork off, total volume of the crate less than two qms.
Hope that's good for a start, please feel free to ask lots of questions.
Greetings, Patrick www.transasia.at