So like the guy that had a Nissan Skyline, with a Toyota 2JZ engine swap, that is not a legal import under Code E on the 3520-1. That vehicle would need to be certified under the mod and test program(Code C) with an Independent Commercial Importer (ICI). If you knowingly import that car, then you are subject to fines and seizure. See below for the relevant parts.
First the penalties
Any person who improperly imports a motor vehicle or engine may be fined up to $32,500 per vehicle or engine, and may be subject to forfeiture of the entire importation bond, and US Customs Service may seize the engine or vehicle.
By signing the document, the importer declares that all information provided is correct, and you authorize the EPA officers to conduct inspections or testing as required by the Clean Air Act.
If the vehicle is at least 21 years old, there are no EPA compliance requirements upon importation. The age of the vehicle is determined by subtracting the calendar year of manufacture from the calendar year of importation. If the calendar year of manufacture is unavailable, the importer may substitute the model year or year of first registration. For instance, to qualify in 2001, the vehicle must have been manufactured in 1980 or earlier. The vehicle must be in its original unmodified configuration. Vehicles at least 21 years old with replacement engines are not eligible for this exemption unless they contain equivalent or newer EPA certified engines.
No approval or Customs bond is required by EPA. The importer must also prove to Customs, as required, that the vehicle or engine was manufactured prior to EPA regulation. Documents such as a title, or letter from the original manufacturer may be used for this purpose.The importer must file with Customs, upon entry, an EPA Form 3520-1 and declare code "E" on that form.
The 3520-1 is the EPA form required when importing motor vehicles, and motor vehicle engines to the US. In addition to the 3520-1, you must fill out an HS-7 for the DOT.