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Hi,it sounds from what you are saying that you have got a inturnal falt with the gearbox,im affried the only way to make a propper diagnoses is to take it apart and look at the gear sincros there has to be worn bearings,or teeth on the gears,or the sellector,or something has just manidged to come loose.
I wish you all thhe best.
If it is a four wheel drive check your tail shaft or drive line by securing the vehicles front wheels jack up the rear tires and in park try to rotate the drive line if you can hear the transmission sound like it is going into gear the transfer case could be damaged! If not a four wheel drive pull the transmission dipstick and look to see if the fluid is dark red or metallic grayish color if so then you're clutch disks inside the tyranny have been worn out and it needs to be rebuilt!
A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.
3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.
The lost acceleration is of major concern. Maybe you have lost your water pump. It would work great for a few miles when you start out and then gradually heat up and loose performance. The fluid would eventually boil over? Maybe a bearing on the camshaft is expressing it's discontent and causing extra load for the engine to overcome. Try to determine where the noise is coming from.
The serpentine belt connects the alternator, water pump, power steering, front timing pulley, fan, and front timing pulley. All these components generate a parasitic load on your engine. If the engine has to work harder because of increased load it could be any of these components. I'd definitely check the water pump listening for noise while running. Look for obvious things related to the belt and its' components.
Check the serpentine belt for wear. May indicate pulley misalignment or wear. There exists two idler pulleys that have small bearings that wear out and squealing noises. Check those for wobble with the tension off the belt. They are pretty cheap so replace them if any concern at all.
Power steering pumps cavitate and make a high pitch gear whining sound if fluids are low or gears warn of. Check the fluid and top off to the correct level.
A gearbox problem is possible but not likely. You are probably hearing pre-ignition aka; engine knock and detonation. Hot carbon deposits on the piston and head are igniting the gas before the spark plug does. Use premium gas instead of regular. Change gearbox oil (10w40). Get a new spark plug one heat range colder than the stock plug for your bike. Chances are the problem will go away once you are using premium gas and have the new plug.
2 things I would inspect, your motor mounts, and CV joints. If worn, one or both could cause what your experiencing. See if you can figure out where grinding is coming from, right or left side & check drive shaft CV joint on that side especially. Look close at both boots on them for rips or holes, where dirt has been entering.
P.S. a sloppy/worn CV joint can end up causing irregular wear on transmission as well, so don't let it go too long, if at all.