You can't use SPI_PPM, these pins are not connected to the 2560.
You can't test the signal levels with a multimeter! You need a scope to see what the peak voltage is when the SPI bus is active.
If Vcc is 5V, the SPI controller will try to drive SCK and MOSI to 5V. When the chip select pin is in output mode it will also be driven toward 5V.
The SD card is a 3.3V device and should not be driven with 5V signals. The actual voltage on SD pins will depend on how much current the SD sinks.
The typical "Absolute Maximum Rating" for SD input voltage is Vdd + 0.3V. If the SD card has a Vdd of 3.3V, this is 3.6V.
Note: Some cards will tolerate 5V input but not all cards will.