Excellent question, first off if you plan on building a blown motor, Nitrous, or turbo, you need to start off with a strong motor, rebuilt or freshened in some way.
Supercharging effects your motor in several ways, first obviously the increased cylinder pressures, many purpose built blower motors have decreased compression ratio, such as 8.5:1, bearing surfaces are always stressed as compared to naturally aspirated, etc.
big improvements to the fuel system are required, the list goes on and on, what you need to do is really think what you want ultimately from the car and go from there.
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