If I can't re-use the pins, then what are my options?
If I was you, I will keep the SD shield and pins setting as is. Only the motor control will be re-build or reconnected and posibility re-code to take into account the new pins for the motor "shield" circuit.
It looks like SD is going to conflict with the motor. The shield docs I have say that the SD shield needs D4, D11,D12,D13 and the Motor shield wants D3,D8,D9,D11,D12,D13, and A0,A1.
SD : keep D4, D11, D12, D13 For the motor "shield" ( may be build on a new DIY board ) , use D2, D3, D5, D6, D7, D8, D9, D10 and all the analogs pins.
Sorry, that the only idea I can think of...