Yes, a TII swap is a whole new motor. The turbo engines are 4 port, NA engines are 6 port. A cold air intake won't help as much as you would think on an FC.
If you want to clean it up, and live in an area with no emissions, strip all that crap off.
If you keep it NA, ditch the stock intake manifold and fuel injection and go with ITB's and a Megasquirt.
Have fun, check out the FAQ at the top of the 2nd Gen section for a whole lotta information!
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1976 Mazda Cosmo RX-5
1976 Mazda Cosmo RX-5
2003 Toyota Tundra TRD
2015 Toyota 4Runner SR5
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