Sounds like you found the cause of the problem. I would install Ford's original air induction system and filter (change every 10,000 miles). Check your turbo--turbine blades may be bent. Air restrictions can take out a turbo in a heartbeat.
Other tips:
. Change coolant (32 qts.) every two years, using a 50/50 mixture of approved antifreeze (Ford Premium Green) and distilled water. Add 10 oz. of Supplemental Coolant Additive (FW-16) every 15,000 miles. This will help prevent cavitation problems. Disconnect batteries and remove 2 hex head engine drain plugs. One is above starter and one is on driver's side. Rear two cylinders are prone to cavitation.
. Change ATF and filter every 30,000 miles with Mercon ATF. On 1999 F-250 trucks, it's easy to drain the converter. I prefer to use Mobil 1 Full Synthetic Multi-Vehicle ATF or either Amsoil's Torque Drive or Universal Synthetic ATF.
Change synthetics every 60,000 miles. With the standard 26 plate ATX cooler, total fill is 17.7 qts; initial fill is 6.5 qts. Pan gasket is reuseable and should be tightened to 11 ft.-lbs.
. Change brake fluid every two years--easy job. Valvoline SynPower Brake Fluid is Ford HBH approved and what I use on PSDs. Remove left-rear off-the-road protection bracket to gain access to the bleeder screw.
. Change fuel filter every 15,000 miles.
. Power Steering Unit--Change and refill with Mobil 1 Synthetic Multi-Vehicle ATF.
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