If the noise is coming from the torque converter, then this may be your problem.
Be advised that this will be at your cost.
A/T - 4R100 Rattling Noise From Torque Converter Area
^ NOISE - "RATTLING" NOISE FROM CONVERTER AREA - VEHICLES EQUIPPED WITH 4R100
TRANSMISSION AND 7.3L DIESEL ENGINE
^ TRANSMISSION - 4R100 - "RATTLING" NOISEFROM CONVERTER AREA - VEHICLES EQUIPPED
WITH 7.3L DIESEL ENGINE
1999 F-250 HD, F-35O, SUPER DUTY F SERIES
A "rattling" noise in the converter housing area when the torque converter clutch is not engaged may occur on some vehicles. This may be caused by impact between the converter piston and cover spline teeth internal to the cover.
Replace the torque converter. The revised torque converter incorporates a new piston and damper design which reduces the possibility of impact between the clutch piston and cover spline teeth.