It may be possible that you have shorted the MISO pin to ground, or that you are applying some sort of loading to that pin. I, too, have had some trouble with a custom board and the MC1321x. I think a lot of it had to do with loading the test pins, although my results were somewhat sporadic. Sometimes I could look at the serial communication between the modem and mcu, other times I couldn't. The clincher for me was figuring out that on one of my boards, by loading the IRQ pin with the scope, I flatlined all the other SPI lines. Do you have test points for the test pins on the MCU? The MC1321x reference manual doesn't tell you what they correspond to (merely saying that you're not supposed to connect them. Another hint, I think), but they are, as found in a reference design provided by Freescale:
Pin 65: PTE5/SPICLK
Pin 66: PTE4/MOSI
Pin 67: PTE3/MISO
Pin 68: PTE2/CE_B
Pin 69: IRQ/IRQ
Pin 70: PTD1/RXTXEN
Pin 71: PTD3/RST_B
Do you have another board that you could try SMAC on?
Hope that helps.