both the due & the pi are 3.3vdc so no level shifter requierd
i don't understand your question -
are you asking about the the spi periperal ? the xmit & recv are shared between periperials (of which you can have upto 15**)
or are you asking about other spi - the usarts can be used as spi ...
I heard only quarter of clock speed of board can be configured for SPI. If 42MHz u mean SPI_CLOCK_DIV2 right?
For question 3, as mentioned in datasheet there are 4 Tx,Rx available physically(0,1,14-19). Im asking about 6 SPI channels? I able to find only one spi channel of pins (MOSI 75,MISO 76,SCk 74). What about other physically?
Question 4: Maximum SPI clock speed in Rpi is 16MHz so need to configure Arduino Due to 16MHz. How to do it if possible?
from the data sheet AT91SAM3x shows 2 'pure' SPI (Table 33-2,33-3) & 4 'USART' SPI (Table 36-1+36-3)
the USART & pure SPI are not setup the same way - esp for DMA /PDC
& as far as the wiring you would have to trace the info in the tables above to see if they are all brought out to aa location that is useable
many lines have mutiple functions
from the data sheet it does look like you could program spi clk to be MCLK/1 but i doubt many perhierals could tolerate that ...
which is slave which is master between the PI & DUE ?
master will set the clock slave doen't care (as long as it is fast enough ...)