Besides the parts already listed, you'll also need the manual trans driveshaft, the ECU from a 98-00 3.0 with a manual ( or a handheld tuner and somebody that knows how to delete the auto trans stuff from your stock ECU), and you'll probably want the steering column trim so that you can remove the column shifter.
Also, make sure the clutch pedal position sensor is tucked up under your dash. Most auto trans trucks had the sensor anyway, but some (like mine) did not. If you have it, the swap will be pretty straightforward. If its not there, then things get tricky and you'll need lots of wiring diagrams.