Cape GPIO usage -- are there reserved pins?

OK, I have designed a cape, a Quad Stallmotor controller with/sense, which
uses 8 GPIO lines: four as outputs to drive a "stallmotor" type of switch
motor for model railroad turnouts [switch tracks] and four inputs to sense
the current state of the stallmotor (the state of the switches).

The I/O pins I am using are:

// GPIO0_7: P9-42
// GPIO1_6: P8-3
// GPIO1_28: P9-12
// GPIO1_7: P8-4

// GPIO1_16: P9-15
// GPIO1_17: P9-23
// GPIO3_21: P9-25
// GPIO3_19: P9-27

I am testing the cape and I having some issues and wanted to check if there
are problems with using these pins, partitularly GPIO1_6 on P8-3 and GPIO1_7
on P8-4 and I am slightly confused about GPIO0_7 on P9-42 (P9-42 seems to be
listed as P9-42a and P9-42b).

I am getting kernel error messages relating to mmcblk1 (I am not using mmcblk1
and I have zeroed it). I *think* this might be because what is "wired" to
P8-3 and P8-4.

Should I be looking at redesigning my cape to use other GPIO lines?

Hi Robert,