I found this when searching for the same thing myself about 6 months ago. Hopefully it will be helpful and let you know how to get it exported from Japan in the first place.
Also, you can go to a good clearing / forwarding agent and talk to them before you begin the whole process. Clearing / Forwarding Agents will help you clear imported goods from the customs and forward them to your address. They will also guide you on what the customs charges other than import duties. As I found out from the FBR website, import duties are 35% on scrap parts in an unpressed condition. Link to the latest tariff is as under.
I wanted to modify my PKDM Cuore, 2006. Searched for a 1996 Daihatsu Mira TR-XX (Turbo version with an EF-DET engine pushing 63 BHP) which is the same as our PKDM Cuore with a 660cc engine, two door version. Just wanted the engine and a better dashboard.
Found out that it costs 390,000 Yen, which is about 3,471 USD or 365k PKR for a clean example. Import duty is 1,215 USD or 128k PKR. Excluding other charges like dismantling, packing, shipping, transport, taxes and others, it comes to 493k. Include those and you'll be looking at something around the region of 600k. I can get a very good 2006 Cuore for 500k with next to nothing required to be done on it.
So I didn't go for an import of parts but went to the used engines market in Quetta instead as I was in Quetta for an Audit. Found the same engine, for 25k from Quetta. Fitting and electrics cost me another 10k. 35k and good to go. Later on, I'm planning to add 4 doors, a complete dashboard, 4 wheels with alloy rims, re-carpet the car and get a new bonnet with an intercooler scoop. Total cost for all this? 12k for the doors, 10k for the dash, 20k for the wheels and 5k for the carpet, brand new. Total cost? 82k. Labor, add another 5k for everything. Add a paint job if I'm inclined and what will that be - another 30k. 120k as compared to 600k and then additional labor costs.
The reasons why importers can do it is bulk purchase, shipping and everything. Also, they may declare the scrap as pressed which reduces the customs duty to 3% and saves them a considerable amount, while paying something to the customs inspector to ignore the condition of the goods. The bribery is purely conjecture on my part, btw. They also do a lot of under-invoicing (trust me on this as I'm an Auditor in a bank and I know this game all too well). I can go on all day about the under-invoicing. 390k yen written as 39k yen. Seen it all too often.