The main thing you need is someone to help you, buying a car off a workshop establishes a relationship which may help you get dodgy shaken and assistance with things like transport and paperwork, you will probably pay normal prices for parts but when you crash in the hills or Setonai Circuit and are looking at a 100,000yen retail tow charge to get home you will find that paying market price for some tiny parts suddenly seems like a really good trade off for a free/cheap tow home from your friendly workshop. Again it depends what you want to do...
If you want to drive/drift/race then do something with a workshop, you may not have to buy a car off them to establish pet gaijin status but it would certainly help.
If you just want a car to cruise around in then you can do it yourself. goo-net is fun to shop around on but you probably won't find any bargains there and a dealer won't want to see you back after you buy the car.
Again, it depends what you want to do...
JIN looks dodgy because it does VIP cars so they could be legitimate businessmen.
What do you want to do with the car?