5.9 Magnum out of manual truck going to work?

If you're going to use the fuel injection from the Magnum motor, you will need to swap the magnetic pickup thing that bolts to the back of the motor, and sits close to the flywheel. They are different lengths for a stick and automatic. Use a stock 5.9 flex plate as others have said. Be sure to line up the torque converter before you install the flex plate. Three of the bolt holes on the 904 converter will line up, and you will have to file the hole out on the flex plate so the 4th one fits.