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metal shavings indicate mechanical failure of the internals
you don't mention the make and model of the transmission but from experience some transmission have a badly designed band servo housing the is prone to breaking at the adjustment area
this gives a clunk as the bands are engaged , band slippage and drops metal into the pan
The fix is generally in car and relatively cheap
pull the pan and check for cracks in the internal castings around the band adjustment screw area
If it is more, have it diagnosed by an accredited specialist transmission shop and get a detailed quote for repairs before you accept the " tranny is s***** answer , need a new one" answer
As you have rebuilt the transmission and now that is working as required , the problem may be in the back lash of the diff side gears or loose drive shaft splines or "U" joints are worn. Check the condition of the engine mounts as well
Check the play in rear end. This is a common problem in Ford truck and vans. chock blocks in front and rear of tires or set parking brake. Put truck in neutral twist drive shaft to see how much it moves. The more movement the more play. The only way to get rid of the noise is to readjust the rear end. This should only be done by a qualified auto tech because of the tools needed to check backlash of the ring and pinon gears. It will more than likely need to have shims put in. Cost wise I would replace it with a good used one or just live with the clunk. I also believe your gears are worn too so if you have it adjusted I would spend the money and put in new gears and bearing set.
Hope this helps you
The clutch may need to be adjusted or replaced, as it sounds like it is not completely releasing. That can also cause the "Clunk" as everything tightens up when trying to find a gear. Although, the clunk is most likely caused by a worn U-Joint. Try to adjust the clutch first.
well i would check your universal joint's put the parking brake on and block the wheels put the car in n and reach under truck and see if there is play in universal if so need replacement if you have two peace drive shaft check your center support bearing good luck if these check good it could be in transmission good luck redoil
The u-joints could cause the banging when you put it in gear. You might want to check the kick down cable. If it's out of ajustment it can cause the hard shift. The transmission thinks the motor is going faster then what it is and will shift harder. Put the car up on jack stand in the rear and put the tranny in neutral.turn the drive shaft back and forth with your hand and see if you hear the clunk or bang you heard when you put it in gear. if not then I would go with the kick down cable being to tightor to short on ajustment. However you want to look at it.