Replying go myself, just for a record here.

I found that sdFat library can be configured to use software SPI on any digital pins.
So now both ShiftMatrixPWM and sdFat are running on the same arduino.
No problems so far contolling just a couple of leds in the prototype.

Hello,

I am working on my first Arduino project, a 16 x 16 monochrome led matrix controlled with ShiftMatrixPWM. All is going fine, but I am afraid I will run out of memory since 32k memory on my Uno is too small to store all the patterns to be displayed on the led matrix. MicroSD cards also use spi and are conflicting with ShiftMatrixPWM.

While waiting for a non-spi ShiftMatrixPWM, I am asking if there is any way to use a sd card reader, even if it means that the led matrix periodically gets disconnected for a moment while sd card is accessed (reading only)?