The "special vehicle registration" is for completely new specially constructed vehicles that have never before been registered. Mostly full reproduction street rods and kit cars. For an engine swap the engine must be the same model year of newer than the chassis, and the engine must have been offered in that "class" of vehicle. ie 1/2 ton truck, not necesarily the same brand/make.
Find your local referee and call them up. The one here in SoCal Riverside was very helpfull.
