You are making things confusing by mixing 40 MegaHertz and 40 kiloHertz.
Arduino only runs at 16 MHz; sampling at 3 MHz is not possible without using an external highspeed ADC, and creating a 40 MHz source is also not possible without an external source.
This one might meet your needs
http://www.analog.com/static/imported-files/data_sheets/AD7276_7277_7278.pdf
if you run the SPI at a high rate.