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I am assuming that you used el cheapo oil filter rather than a known brand in the service. Oil filters have a non drain back valve built into the filter to stop your problem but some cheap or wrong filters do not have this valve hence your problem.. The noise goes when the oil pressure fills up all the hydraulic lifters and oil pressure is achieved.
CLATTERING NOISE COULD BE WORN LIFTERS OR OIL CONTAMINATED WITH ANTIFREEZE OR GASOLINE.OR THE OIL PASSAGES IN BLOCK STOPPED UP WITH SLUDGE.TRY CHANGING ENGINE OIL AND FILTER ADD A CAN OF SEAFOAM TO CRANK CASE.DONT OVER FILL CRANK CASE.IF CLATTERING DOES STOP NEW OIL GET REAL BLACK DIRTY.YOU PROBABLY NEED TO CHANGE OIL FILTER AND OIL AGAIN.WHEN SEAFOAM CIRCULATE THROUGH THE ENGINE BLOCK FLUSHING OUT CARBON SLUDGE BUILD UP IN OIL PASSAGES.IT WILL GO TO OIL CRANK CASE GETTING NEW OIL DIRTY.SO CHANGE ENGINE OIL AGAIN.ONCE LIFTERS QUIET DOWN.IF LIFTERS NOISE CONTINUE.YOU NEED NEW LIFTERS.
not completely sure it has something to do with the auto trans, but more likely the hydraulic lifters. the older cars used to have a fixed valve clearance with tappets, but now they use hydraulic lifters. the problem with these is if you don't change the oil at a regular interval or do alot of stop-start driving, the oil becomes sludgy and does not flow into the small tolerance holes in the lifters. the beautiful thing about oil is that it thins out as it gets hotter to a point, so as the engine warms up, the oil thins out and flows into the lifter hydraulically pumping them up and closing the gap, i would suggest to change the engine oil to manufacturer's specs and add a "lifter free" product, after a few weeks it will reduce dramatically
There are two mechanical noises you will hear from an engine, lifter noise, wrist pin slap, and rod bearing noise. The only one that will go away, if at all, with engine warm-up, is lifter noise. All assuming of course, the noise is coming from the engine, and not any of the externally mounted accessories. Have the oil changed, and continue to change every 2000-3000 miles with a good quality oil, maybe the lifter will clear itself. If it does, maintain the oil changes for the next few changes to assure it is cleaning out. You might also try adding 1-2 pints Berrymen's Chemtool to the oil 200-300 miles before you plan to change the oil.
What kinda batteries do you got? Are the cables any good? Sounds to me like a power/ground issuse. Either that or you have to small of batteries to crank over a high compession enigne when it's cold, with the glow plugs, and heater grid pulling all of the power from the batteries.
And check the trans fluid level for your problem with the trans.
And you're gonna need to be a little more specific on the thunping noise.
HAVE YOU CHANGED OIL REGULARLY?WHAT ENGINE?4.7L:YOU MAY HAVE A STICKY LIFTER OR A TIMING CHAIN TENSIONER ISSUE..I WOULD CHANGE THE OIL AND FILTER AND PUT SOME ADDITIVE IN ENGINE(LUCAS SEEMS TO WORK)
5.7L:LIFTER OR SOME PISTON SLAP..LET ME KNOW WHAT ENGINE IS IN VEHICLE AND SOME MORE INFO WOULD BE GOOD
Lifters on your engine are non-adjustable. If noise is not loud or is intermittent, sometimes just changing oil and using an additive like marvel oil will clean it up.If noise persists, check pivot contact points on "bridge" that connects each pair of rocker arms together for wear.Replace if worn. disable the ignition system and have someone crank engine over. Observe that all rockers are going up and down the same distance. The ones to check are the ones that are not. If all is ok there, you must go deeper into engine and check lifters for end wear. If you find wear, lifter and camshaft must be replaced Sometimes if the ends are still in good condition, the lifter itself may have an internal problem.If that is the case, replace the lifter. Before you begin, check oil pressure. A pressure of 15lbs or less is not acceptable.(warmed up, at idle) Pressure must be substantially higher both cold and hot. I recommend at least 30psi at idle hot, 40psi while driving. Lower pressures indicate serious wear on internal bearing surfaces. Replacing the oil pump may temporarily hide this problem but will not cure it!!! Good luck