Jeff,

That sounds like some serious deterioration of your engine, especially since you change the oil only every 3 months. Diesel engines contaminate the oil twice faster than do gas engines, and therefore need an oil change in half the time(or twice as often). Lumakas ba ang usok dun sa tailpipe? Yung grinding noise, can that be heard only when the car is accelerating or decelerating while in gear with the clutch fully released? If so, it could be that your engine is hitting the chassis when torque is applied. This is caused by weak/damaged engine support/s. A faulty release bearing only makes noises when clutch pedal pressure is applied.