the most basic difference is that JDM is more expensive...if i were you, i would just buy a usdm GSR motor, or a usdm ITR motor (thats the swap i have, mucho fasto)
dont waste your money on JDM stuff, its all overrated, and most people that claim to be jdm, arent even close...except for this one guy on here, i forget his name, RiceBoy or something...he has about as close to a car being truly JDM as you can get