Aron, when you start looking at the PCB layout could I ask for one small change? Could you add a 22k pullup resistor from J4 pin 3 (DD7 on the IDE bus) to +5V. Let me explain.
I have redeveloped the software to handle two drives on the IDE bus (master & slave) and that all works. However, I really need to be able to detect whether a slave device is installed or not. If there is no slave unit and I try to address it then the bus will float in an indeterminate state. DD7 is the busy bit for a status read so if I find it high then I know that the slave is not installed or faulty.
If it is not possible then I can always solder a resistor on the prototype board.
Thanks
Mike