Stock aircraft have there pilots as apart of the model. You have to make the pilots invisable by using alpha layers on the ja_pilot_1.bmp, ja_pilot_2.bmp or US_pilot_1.bmp us_pilot_1.bmp. Place the ja_pilot_1.bmp, ja_pilot_2.bmp or US_pilot_1.bmp us_pilot_1.bmp into the aircraft's texture folder.
DP based pilot sticking out sound like bad mounting points for it in the DP. You will need to move the mount.